Table of SynGAP1 Isoform α2 (UniProt Q96PV0-1) Missense Variants.

c.dna	Variant	Domain	ClinVar			gnomAD			ESM1b		AlphaMissense			REVEL		FoldX			Rosetta		Foldetta		PremPS		PROVEAN		PolyPhen-2 HumDiv		PolyPhen-2 HumVar		FATHMM		SIFT				PAM		Physical		SASA		Normalized B-factor backbone		Normalized B-factor sidechain		SynGAP Structural Annotation									DOI
			Clinical Status	Review	Subm.	ID	Allele count	Allele freq.	LLR score	Prediction	Pathogenicity	Class	Optimized	Score	Prediction	Average ΔΔG	Prediction	StdDev	ΔΔG	Prediction	ΔΔG	Prediction	ΔΔG	Prediction	Score	Prediction	pph2_prob	Prediction	pph2_prob	Prediction	Nervous System Score	Prediction	Prediction	Status	Conservation	Sequences	PAM250	PAM120	Hydropathy Δ	MW Δ	Average	Δ	Δ	StdDev	Δ	StdDev	Secondary	Tertiary bonds	Inside out	GAP-Ras interface	At membrane	No effect	MD Alert	Verdict	Description
c.103G>A	V35I					6-33423512-G-A	5	3.10e-6	-3.764	Likely Benign	0.081	Likely Benign	Likely Benign	0.017	Likely Benign										-0.32	Neutral	0.672	Possibly Damaging	0.369	Benign	4.16	Benign	0.00	Affected	4.32	1	3	4	0.3	14.03
c.103G>C	V35L					6-33423512-G-C	4	2.48e-6	-2.893	Likely Benign	0.108	Likely Benign	Likely Benign	0.039	Likely Benign										-0.58	Neutral	0.481	Possibly Damaging	0.506	Possibly Damaging	4.18	Benign	0.00	Affected	4.32	1	1	2	-0.4	14.03
c.106C>T	H36Y		Uncertain		1	6-33423515-C-T	2	1.24e-6	-3.461	Likely Benign	0.139	Likely Benign	Likely Benign	0.023	Likely Benign										-1.03	Neutral	0.219	Benign	0.066	Benign	4.16	Benign	0.00	Affected	4.32	1	0	2	1.9	26.03
c.110C>A	S37Y					6-33423519-C-A	1	6.20e-7	-4.447	Likely Benign	0.370	Ambiguous	Likely Benign	0.132	Likely Benign										-1.61	Neutral	0.880	Possibly Damaging	0.888	Possibly Damaging	3.90	Benign	0.00	Affected	4.32	1	-2	-3	-0.5	76.10
c.113C>T	P38L		Conflicting		4	6-33423522-C-T	8	4.96e-6	-2.469	Likely Benign	0.197	Likely Benign	Likely Benign	0.141	Likely Benign										-2.56	Deleterious	0.983	Probably Damaging	0.931	Probably Damaging	4.02	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.11C>A	S4Y					6-33420275-C-A			-5.156	Likely Benign	0.209	Likely Benign	Likely Benign	0.099	Likely Benign										-0.34	Neutral	0.880	Possibly Damaging	0.608	Possibly Damaging	4.12	Benign	0.00	Affected	4.32	1	-2	-3	-0.5	76.10
c.121C>T	R41C		Conflicting		3	6-33423530-C-T	7	4.34e-6	-4.745	Likely Benign	0.207	Likely Benign	Likely Benign	0.093	Likely Benign										-1.10	Neutral	0.976	Probably Damaging	0.919	Probably Damaging	4.13	Benign	0.00	Affected	4.32	1	-4	-3	7.0	-53.05
c.122G>A	R41H					6-33423531-G-A	6	3.72e-6	-4.425	Likely Benign	0.106	Likely Benign	Likely Benign	0.059	Likely Benign										-0.74	Neutral	0.976	Probably Damaging	0.848	Possibly Damaging	4.17	Benign	0.00	Affected	4.32	1	0	2	1.3	-19.05																10.1016/j.ajhg.2020.11.011
c.124C>T	P42S					6-33423533-C-T	1	6.20e-7	-3.472	Likely Benign	0.109	Likely Benign	Likely Benign	0.048	Likely Benign										-1.12	Neutral	0.909	Possibly Damaging	0.901	Possibly Damaging	4.24	Benign	0.00	Affected	4.32	1	-1	1	0.8	-10.04
c.127G>A	G43S		Uncertain		2	6-33423536-G-A	1	6.20e-7	-3.301	Likely Benign	0.078	Likely Benign	Likely Benign	0.057	Likely Benign										-0.30	Neutral	0.162	Benign	0.096	Benign	4.29	Benign	0.00	Affected	4.32	1	1	0	-0.4	30.03
c.128G>C	G43A					6-33423537-G-C	2	1.24e-6	-3.925	Likely Benign	0.073	Likely Benign	Likely Benign	0.026	Likely Benign										-0.52	Neutral	0.001	Benign	0.005	Benign	4.29	Benign	0.00	Affected	4.32	1	0	1	2.2	14.03
c.136C>T	P46S		Uncertain		1				-3.338	Likely Benign	0.302	Likely Benign	Likely Benign	0.066	Likely Benign										-0.60	Neutral	0.909	Possibly Damaging	0.901	Possibly Damaging	4.15	Benign	0.00	Affected			1	-1	0.8	-10.04
c.137C>G	P46R					6-33423546-C-G	1	6.20e-7	-0.520	Likely Benign	0.385	Ambiguous	Likely Benign	0.155	Likely Benign										0.39	Neutral	0.972	Probably Damaging	0.954	Probably Damaging	4.39	Benign	0.00	Affected	4.32	1	-2	0	-2.9	59.07
c.139C>T	R47W					6-33423548-C-T	1	6.20e-7	-9.201	Likely Pathogenic	0.752	Likely Pathogenic	Likely Benign	0.201	Likely Benign										-2.17	Neutral	0.994	Probably Damaging	0.919	Probably Damaging	4.00	Benign	0.00	Affected	4.32	1	-3	2	3.6	30.03
c.13C>G	R5G		Uncertain		1				-3.639	Likely Benign	0.149	Likely Benign	Likely Benign	0.169	Likely Benign										-0.16	Neutral	0.013	Benign	0.003	Benign	4.12	Benign	0.00	Affected	4.32	1	-2	-3	4.1	-99.14
c.140G>A	R47Q		Likely Benign		1	6-33423549-G-A	4	2.48e-6	-4.989	Likely Benign	0.347	Ambiguous	Likely Benign	0.096	Likely Benign										-0.57	Neutral	0.829	Possibly Damaging	0.614	Possibly Damaging	4.12	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06																10.1016/j.ajhg.2020.11.011
c.14G>A	R5Q					6-33420278-G-A	2	1.30e-6	-4.261	Likely Benign	0.223	Likely Benign	Likely Benign	0.094	Likely Benign										-0.06	Neutral	0.403	Benign	0.007	Benign	4.15	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06
c.155C>T	S52L		Uncertain		1	6-33423564-C-T	1	6.20e-7	-7.199	In-Between	0.688	Likely Pathogenic	Likely Benign	0.087	Likely Benign										-1.41	Neutral	0.829	Possibly Damaging	0.706	Possibly Damaging	4.10	Benign	0.00	Affected	4.32	1	-3	-2	4.6	26.08
c.163C>A	Q55K		Uncertain		2	6-33423572-C-A	24	1.49e-5	-5.840	Likely Benign	0.612	Likely Pathogenic	Likely Benign	0.085	Likely Benign										-1.21	Neutral	0.140	Benign	0.184	Benign	3.91	Benign	0.00	Affected	4.32	1	1	1	-0.4	0.04
c.164A>C	Q55P					6-33423573-A-C	1	6.20e-7	-13.163	Likely Pathogenic	0.897	Likely Pathogenic	Ambiguous	0.260	Likely Benign										-2.06	Neutral	0.462	Possibly Damaging	0.480	Possibly Damaging	3.83	Benign	0.00	Affected	4.32	1	-1	0	1.9	-31.01
c.169C>T	L57F		Uncertain		2				-5.096	Likely Benign	0.459	Ambiguous	Likely Benign	0.051	Likely Benign										-0.78	Neutral	0.824	Possibly Damaging	0.879	Possibly Damaging	3.96	Benign	0.00	Affected	4.32	1	2	0	-1.0	34.02
c.16G>A	A6T					6-33420280-G-A			-3.711	Likely Benign	0.130	Likely Benign	Likely Benign	0.089	Likely Benign										-0.13	Neutral	0.027	Benign	0.004	Benign	4.11	Benign	0.00	Affected	4.32	1	0	1	-2.5	30.03
c.16G>T	A6S					6-33420280-G-T			-2.485	Likely Benign	0.082	Likely Benign	Likely Benign	0.097	Likely Benign										0.06	Neutral	0.001	Benign	0.001	Benign	4.17	Benign	0.00	Affected	4.32	1	1	1	-2.6	16.00
c.172A>G	M58V		Uncertain		1				-2.211	Likely Benign	0.688	Likely Pathogenic	Likely Benign	0.160	Likely Benign										-0.71	Neutral	0.006	Benign	0.091	Benign	4.19	Benign	0.00	Affected	4.32	1	1	2	2.3	-32.06
c.173T>C	M58T					6-33423582-T-C	1	6.20e-7	-4.308	Likely Benign	0.980	Likely Pathogenic	Likely Pathogenic	0.159	Likely Benign										-1.58	Neutral	0.018	Benign	0.184	Benign	4.09	Benign	0.00	Affected	4.32	1	-1	-1	-2.6	-30.09
c.174G>A	M58I					6-33423583-G-A	1	6.20e-7	-2.153	Likely Benign	0.971	Likely Pathogenic	Likely Pathogenic	0.078	Likely Benign										-0.55	Neutral	0.006	Benign	0.091	Benign	4.21	Benign	0.00	Affected	4.32	1	1	2	2.6	-18.03
c.17C>A	A6D					6-33420281-C-A			-3.340	Likely Benign	0.209	Likely Benign	Likely Benign	0.211	Likely Benign										0.34	Neutral	0.117	Benign	0.010	Benign	4.07	Benign	0.00	Affected	4.32	1	-2	0	-5.3	44.01
c.17C>T	A6V					6-33420281-C-T			-3.781	Likely Benign	0.191	Likely Benign	Likely Benign	0.123	Likely Benign										0.32	Neutral	0.117	Benign	0.007	Benign	4.09	Benign	0.00	Affected	4.32	1	0	0	2.4	28.05
c.184G>A	D62N					6-33423593-G-A	1	6.20e-7	-4.607	Likely Benign	0.207	Likely Benign	Likely Benign	0.075	Likely Benign										-1.08	Neutral	0.028	Benign	0.032	Benign	4.11	Benign	0.00	Affected	4.32	1	1	2	0.0	-0.98
c.187G>A	E63K		Uncertain		1				-4.976	Likely Benign	0.894	Likely Pathogenic	Ambiguous	0.103	Likely Benign										-0.70	Neutral	0.458	Possibly Damaging	0.678	Possibly Damaging	3.98	Benign	0.00	Affected	4.32	1	1	0	-0.4	-0.94
c.187G>C	E63Q		Uncertain		1				-4.038	Likely Benign	0.687	Likely Pathogenic	Likely Benign	0.078	Likely Benign										-0.85	Neutral	0.659	Possibly Damaging	0.775	Possibly Damaging	3.90	Benign	0.00	Affected	4.32	1	2	2	0.0	-0.98
c.191T>C	I64T					6-33425799-T-C	1	6.20e-7	-3.183	Likely Benign	0.943	Likely Pathogenic	Ambiguous	0.075	Likely Benign										-0.51	Neutral	0.092	Benign	0.007	Benign	4.08	Benign	0.00	Affected	4.32	1	-1	0	-5.2	-12.05
c.192A>G	I64M					6-33425800-A-G	2	1.24e-6	-4.327	Likely Benign	0.523	Ambiguous	Likely Benign	0.047	Likely Benign										-0.05	Neutral	0.637	Possibly Damaging	0.047	Benign	4.04	Benign	0.00	Affected	4.32	1	1	2	-2.6	18.03
c.194A>G	H65R		Uncertain		1	6-33425802-A-G	1	6.20e-7	-1.980	Likely Benign	0.967	Likely Pathogenic	Likely Pathogenic	0.073	Likely Benign										-1.60	Neutral	0.462	Possibly Damaging	0.227	Benign	4.19	Benign	0.00	Affected	4.32	1	2	0	-1.3	19.05
c.195C>A	H65Q					6-33425803-C-A	1	6.20e-7	-2.966	Likely Benign	0.953	Likely Pathogenic	Ambiguous	0.035	Likely Benign										-1.46	Neutral	0.462	Possibly Damaging	0.227	Benign	4.19	Benign	0.00	Affected	4.32	1	0	3	-0.3	-9.01
c.196C>G	P66A		Uncertain		1				-2.845	Likely Benign	0.891	Likely Pathogenic	Ambiguous	0.091	Likely Benign										-1.56	Neutral	0.805	Possibly Damaging	0.539	Possibly Damaging	4.04	Benign	0.00	Affected	4.32	1	1	-1	3.4	-26.04
c.196C>T	P66S		Benign		1	6-33425804-C-T	2	1.24e-6	-2.760	Likely Benign	0.929	Likely Pathogenic	Ambiguous	0.081	Likely Benign										-1.69	Neutral	0.909	Possibly Damaging	0.641	Possibly Damaging	4.01	Benign	0.00	Affected	4.32	1	1	-1	0.8	-10.04
c.19T>C	S7P					6-33420283-T-C			-3.798	Likely Benign	0.111	Likely Benign	Likely Benign	0.210	Likely Benign										-0.23	Neutral	0.267	Benign	0.029	Benign	4.07	Benign	0.00	Affected	4.32	1	-1	1	-0.8	10.04
c.203T>A	L68Q					6-33425811-T-A	5	3.10e-6	-3.436	Likely Benign	0.826	Likely Pathogenic	Ambiguous	0.119	Likely Benign										-0.14	Neutral	0.943	Possibly Damaging	0.766	Possibly Damaging	4.15	Benign	0.00	Affected	4.32	1	-2	-2	-7.3	14.97
c.205A>T	I69F					6-33425813-A-T	2	1.24e-6	-3.747	Likely Benign	0.251	Likely Benign	Likely Benign	0.104	Likely Benign										-0.99	Neutral	0.824	Possibly Damaging	0.507	Possibly Damaging	4.12	Benign	0.00	Affected	4.32	1	0	1	-1.7	34.02
c.206T>C	I69T					6-33425814-T-C	1	6.20e-7	-2.978	Likely Benign	0.755	Likely Pathogenic	Likely Benign	0.116	Likely Benign										-0.79	Neutral	0.824	Possibly Damaging	0.507	Possibly Damaging	4.15	Benign	0.00	Affected	4.32	1	-1	0	-5.2	-12.05
c.208C>G	R70G					6-33425816-C-G	1	6.20e-7	-3.555	Likely Benign	0.430	Ambiguous	Likely Benign	0.095	Likely Benign										-0.61	Neutral	0.962	Probably Damaging	0.726	Possibly Damaging	4.11	Benign	0.00	Affected	4.32	1	-2	-3	4.1	-99.14
c.209G>A	R70Q					6-33425817-G-A	1	6.20e-7	-3.399	Likely Benign	0.180	Likely Benign	Likely Benign	0.109	Likely Benign										-0.04	Neutral	0.983	Probably Damaging	0.602	Possibly Damaging	4.25	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06
c.212A>G	D71G					6-33425820-A-G	1	6.20e-7	-3.136	Likely Benign	0.439	Ambiguous	Likely Benign	0.111	Likely Benign										-1.82	Neutral	0.171	Benign	0.021	Benign	4.03	Benign	0.00	Affected	4.32	1	-1	1	3.1	-58.04
c.214C>T	R72W					6-33425822-C-T	1	6.20e-7	-5.546	Likely Benign	0.430	Ambiguous	Likely Benign	0.145	Likely Benign										-1.82	Neutral	0.994	Probably Damaging	0.689	Possibly Damaging	4.07	Benign	0.00	Affected	4.32	1	-3	2	3.6	30.03
c.215G>A	R72Q					6-33425823-G-A			-4.413	Likely Benign	0.135	Likely Benign	Likely Benign	0.100	Likely Benign										-0.13	Neutral	0.829	Possibly Damaging	0.238	Benign	4.20	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06
c.218G>A	R73K		Uncertain		1	6-33425826-G-A	2	1.24e-6	-4.033	Likely Benign	0.151	Likely Benign	Likely Benign	0.077	Likely Benign										-0.46	Neutral	0.053	Benign	0.007	Benign	4.14	Benign	0.00	Affected	4.32	1	2	3	0.6	-28.01
c.2194A>G	R732G					6-33441659-A-G	1	6.20e-7	-9.348	Likely Pathogenic	0.295	Likely Benign	Likely Benign	0.145	Likely Benign										-2.98	Deleterious	1.000	Probably Damaging	0.982	Probably Damaging	2.56	Benign	0.03	Affected	3.59	7	-2	-3	4.1	-99.14
c.2195G>A	R732K		Conflicting		2	6-33441660-G-A	4	2.48e-6	-5.278	Likely Benign	0.240	Likely Benign	Likely Benign	0.045	Likely Benign										-0.82	Neutral	0.973	Probably Damaging	0.943	Probably Damaging	2.69	Benign	0.21	Tolerated	3.59	7	3	2	0.6	-28.01
c.2195G>C	R732T		Uncertain		1				-8.545	Likely Pathogenic	0.434	Ambiguous	Likely Benign	0.075	Likely Benign										-1.96	Neutral	0.999	Probably Damaging	0.892	Possibly Damaging	2.59	Benign	0.12	Tolerated	3.59	7	-1	-1	3.8	-55.08
c.2200C>T	P734S		Uncertain		2	6-33441665-C-T	2	1.24e-6	-4.291	Likely Benign	0.077	Likely Benign	Likely Benign	0.030	Likely Benign										-2.44	Neutral	0.344	Benign	0.048	Benign	2.77	Benign	0.11	Tolerated	3.64	6	1	-1	0.8	-10.04																10.1016/j.ajhg.2020.11.011
c.2201C>T	P734L					6-33441666-C-T	3	1.86e-6	-3.472	Likely Benign	0.095	Likely Benign	Likely Benign	0.069	Likely Benign										-2.11	Neutral	0.897	Possibly Damaging	0.330	Benign	2.69	Benign	1.00	Tolerated	3.64	6	-3	-3	5.4	16.04
c.2206C>T	R736C		Conflicting		3	6-33441671-C-T	8	4.96e-6	-7.113	In-Between	0.120	Likely Benign	Likely Benign	0.190	Likely Benign										-2.06	Neutral	0.999	Probably Damaging	0.825	Possibly Damaging	2.48	Pathogenic	0.00	Affected	4.07	3	-4	-3	7.0	-53.05
c.2207G>A	R736H		Uncertain		1	6-33441672-G-A	6	3.72e-6	-5.409	Likely Benign	0.067	Likely Benign	Likely Benign	0.029	Likely Benign										-0.12	Neutral	0.004	Benign	0.001	Benign	2.50	Benign	0.00	Affected	4.07	3	2	0	1.3	-19.05
c.2210A>C	Q737P		Uncertain		1				-2.407	Likely Benign	0.054	Likely Benign	Likely Benign	0.154	Likely Benign										-1.22	Neutral	0.005	Benign	0.013	Benign	2.78	Benign	0.04	Affected	4.07	3	-1	0	1.9	-31.01
c.2212A>T	S738C					6-33441677-A-T	4	2.48e-6	-6.373	Likely Benign	0.081	Likely Benign	Likely Benign	0.058	Likely Benign										-2.09	Neutral	0.975	Probably Damaging	0.815	Possibly Damaging	2.63	Benign	0.01	Affected	4.32	2	-1	0	3.3	16.06
c.2214T>G	S738R		Benign		1	6-33441679-T-G	1	6.20e-7	-4.241	Likely Benign	0.570	Likely Pathogenic	Likely Benign	0.068	Likely Benign										-1.55	Neutral	0.473	Possibly Damaging	0.193	Benign	2.69	Benign	0.01	Affected	4.32	2	0	-1	-3.7	69.11
c.2215G>C	E739Q		Uncertain		1				-2.846	Likely Benign	0.161	Likely Benign	Likely Benign	0.071	Likely Benign										-1.06	Neutral	0.801	Possibly Damaging	0.339	Benign	2.57	Benign	0.00	Affected	4.32	2	2	2	0.0	-0.98
c.2216A>T	E739V		Uncertain		1				-3.136	Likely Benign	0.274	Likely Benign	Likely Benign	0.085	Likely Benign										-1.86	Neutral	0.891	Possibly Damaging	0.575	Possibly Damaging	2.47	Pathogenic	0.00	Affected	4.32	2	-2	-2	7.7	-29.98
c.2218C>T	R740W		Uncertain		2	6-33441683-C-T	6	3.72e-6	-8.561	Likely Pathogenic	0.168	Likely Benign	Likely Benign	0.180	Likely Benign										-3.09	Deleterious	1.000	Probably Damaging	0.938	Probably Damaging	2.52	Benign	0.01	Affected	4.32	2	2	-3	3.6	30.03
c.2219G>A	R740Q		Uncertain		1	6-33441684-G-A	4	2.48e-6	-5.195	Likely Benign	0.078	Likely Benign	Likely Benign	0.102	Likely Benign										-0.67	Neutral	0.999	Probably Damaging	0.881	Possibly Damaging	2.60	Benign	0.08	Tolerated	4.32	2	1	1	1.0	-28.06
c.221G>A	S74N		Uncertain		1	6-33425829-G-A	5	3.10e-6	-5.156	Likely Benign	0.112	Likely Benign	Likely Benign	0.031	Likely Benign										-0.89	Neutral	0.043	Benign	0.007	Benign	4.09	Benign	0.00	Affected	4.32	1	1	1	-2.7	27.03
c.2221C>T	P741S		Uncertain		2	6-33441686-C-T	3	1.86e-6	-3.700	Likely Benign	0.063	Likely Benign	Likely Benign	0.076	Likely Benign										-0.27	Neutral	0.270	Benign	0.136	Benign	2.92	Benign	0.00	Affected	4.32	2	1	-1	0.8	-10.04																10.1016/j.ajhg.2020.11.011
c.2224C>T	R742W		Uncertain		1	6-33441689-C-T	6	3.72e-6	-7.725	In-Between	0.133	Likely Benign	Likely Benign	0.079	Likely Benign										-1.71	Neutral	0.992	Probably Damaging	0.684	Possibly Damaging	2.66	Benign	0.01	Affected	4.32	2	-3	2	3.6	30.03
c.2225G>A	R742Q		Uncertain		2	6-33441690-G-A	24	1.49e-5	-4.090	Likely Benign	0.068	Likely Benign	Likely Benign	0.054	Likely Benign										-0.19	Neutral	0.032	Benign	0.007	Benign	2.73	Benign	0.07	Tolerated	4.32	2	1	1	1.0	-28.06
c.2225G>C	R742P					6-33441690-G-C	1	6.20e-7	-2.920	Likely Benign	0.112	Likely Benign	Likely Benign	0.081	Likely Benign										-0.51	Neutral	0.001	Benign	0.004	Benign	2.84	Benign	0.03	Affected	4.32	2	-2	0	2.9	-59.07
c.2227C>T	P743S					6-33441692-C-T	1	6.19e-7	-4.286	Likely Benign	0.063	Likely Benign	Likely Benign	0.085	Likely Benign										-0.33	Neutral	0.021	Benign	0.015	Benign	2.93	Benign	0.00	Affected	4.32	2	-1	1	0.8	-10.04																10.1016/j.ajhg.2020.11.011
c.2228C>T	P743L					6-33441693-C-T	1	6.19e-7	-4.838	Likely Benign	0.081	Likely Benign	Likely Benign	0.112	Likely Benign										-2.21	Neutral	0.801	Possibly Damaging	0.192	Benign	2.73	Benign	0.00	Affected	4.32	2	-3	-3	5.4	16.04
c.222C>A	S74R					6-33425830-C-A	1	6.20e-7	-3.271	Likely Benign	0.418	Ambiguous	Likely Benign	0.070	Likely Benign										-1.34	Neutral	0.361	Benign	0.019	Benign	4.08	Benign	0.00	Affected	4.32	1	-1	0	-3.7	69.11
c.2233C>T	P745S					6-33441698-C-T	1	6.19e-7	-4.300	Likely Benign	0.077	Likely Benign	Likely Benign	0.160	Likely Benign										-2.32	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	2.54	Benign	0.05	Affected	4.32	2	-1	1	0.8	-10.04
c.2236G>C	V746L					6-33441701-G-C	1	6.19e-7	-3.260	Likely Benign	0.086	Likely Benign	Likely Benign	0.015	Likely Benign										-0.68	Neutral	0.002	Benign	0.003	Benign	2.82	Benign	0.08	Tolerated	4.32	2	1	2	-0.4	14.03
c.2239G>C	V747L		Uncertain		1	6-33441704-G-C	2	1.24e-6	-2.790	Likely Benign	0.096	Likely Benign	Likely Benign	0.047	Likely Benign										-0.52	Neutral	0.065	Benign	0.033	Benign	2.67	Benign	0.00	Affected	4.32	2	2	1	-0.4	14.03
c.223G>A	E75K		Likely Benign		1				-4.020	Likely Benign	0.358	Ambiguous	Likely Benign	0.134	Likely Benign										-1.12	Neutral	0.748	Possibly Damaging	0.017	Benign	4.07	Benign	0.00	Affected			0	1	-0.4	-0.94
c.2243T>C	L748P					6-33441708-T-C	1	6.20e-7	-2.732	Likely Benign	0.129	Likely Benign	Likely Benign	0.075	Likely Benign										-0.69	Neutral	0.912	Possibly Damaging	0.611	Possibly Damaging	2.69	Benign	0.02	Affected	4.32	2	-3	-3	-5.4	-16.04
c.2243T>G	L748R		Conflicting		2	6-33441708-T-G	3	1.86e-6	-3.331	Likely Benign	0.245	Likely Benign	Likely Benign	0.055	Likely Benign										-0.67	Neutral	0.912	Possibly Damaging	0.448	Possibly Damaging	2.73	Benign	0.02	Affected	4.32	2	-3	-2	-8.3	43.03
c.2245C>T	R749W		Uncertain		1	6-33441710-C-T	3	1.86e-6	-7.647	In-Between	0.338	Likely Benign	Likely Benign	0.173	Likely Benign										-2.62	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.59	Benign	0.00	Affected	4.32	2	2	-3	3.6	30.03
c.2246G>A	R749Q		Likely Benign		1	6-33441711-G-A	4	2.48e-6	-3.069	Likely Benign	0.212	Likely Benign	Likely Benign	0.152	Likely Benign										-1.00	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	2.64	Benign	0.03	Affected	4.32	2	1	1	1.0	-28.06
c.2248G>A	G750R					6-33441713-G-A	17	1.05e-5	-3.861	Likely Benign	0.619	Likely Pathogenic	Likely Benign	0.179	Likely Benign										-2.09	Neutral	1.000	Probably Damaging	0.982	Probably Damaging	2.45	Pathogenic	0.00	Affected	3.99	5	-2	-3	-4.1	99.14
c.2249G>A	G750E		Uncertain		1				-2.618	Likely Benign	0.413	Ambiguous	Likely Benign	0.146	Likely Benign										-2.27	Neutral	1.000	Probably Damaging	0.982	Probably Damaging	2.49	Pathogenic	0.01	Affected	3.99	5	0	-2	-3.1	72.06
c.2252C>G	P751R					6-33441717-C-G	1	6.20e-7	-5.646	Likely Benign	0.296	Likely Benign	Likely Benign	0.157	Likely Benign										-2.61	Deleterious	0.719	Possibly Damaging	0.295	Benign	2.68	Benign	0.06	Tolerated	3.99	5	-2	0	-2.9	59.07
c.2255C>T	S752L		Uncertain		2	6-33441720-C-T	6	3.72e-6	-3.386	Likely Benign	0.182	Likely Benign	Likely Benign	0.195	Likely Benign										-2.09	Neutral	0.993	Probably Damaging	0.641	Possibly Damaging	1.51	Pathogenic	0.01	Affected	3.99	5	-3	-2	4.6	26.08
c.2257G>A	A753T					6-33441722-G-A	2	1.24e-6	-4.298	Likely Benign	0.069	Likely Benign	Likely Benign	0.071	Likely Benign										-0.42	Neutral	0.022	Benign	0.018	Benign	2.70	Benign	0.28	Tolerated	3.99	5	0	1	-2.5	30.03
c.225G>C	E75D					6-33425833-G-C	1	6.20e-7	-3.710	Likely Benign	0.073	Likely Benign	Likely Benign	0.058	Likely Benign										-0.27	Neutral	0.001	Benign	0.000	Benign	4.25	Benign	0.00	Affected	4.32	1	2	3	0.0	-14.03
c.226T>G	S76A					6-33425834-T-G	1	6.20e-7	-3.230	Likely Benign	0.072	Likely Benign	Likely Benign	0.048	Likely Benign										-1.10	Neutral	0.643	Possibly Damaging	0.277	Benign	3.86	Benign	0.00	Affected	4.32	1	1	1	2.6	-16.00
c.2273A>C	Y758S					6-33441738-A-C	1	6.20e-7	-1.912	Likely Benign	0.215	Likely Benign	Likely Benign	0.110	Likely Benign										-0.54	Neutral	0.912	Possibly Damaging	0.629	Possibly Damaging	2.75	Benign	0.06	Tolerated	3.99	5	-2	-3	0.5	-76.10
c.2275A>C	M759L		Uncertain		1	6-33441740-A-C	2	1.24e-6	-2.431	Likely Benign	0.093	Likely Benign	Likely Benign	0.048	Likely Benign										-0.53	Neutral	0.002	Benign	0.005	Benign	2.84	Benign	1.00	Tolerated	3.99	5	4	2	1.9	-18.03
c.2275A>G	M759V					6-33441740-A-G	20	1.24e-5	-3.985	Likely Benign	0.074	Likely Benign	Likely Benign	0.030	Likely Benign										-1.00	Neutral	0.267	Benign	0.127	Benign	2.67	Benign	0.23	Tolerated	3.99	5	1	2	2.3	-32.06																10.1016/j.ajhg.2020.11.011
c.2277G>A	M759I					6-33441742-G-A	1	6.20e-7	-4.058	Likely Benign	0.393	Ambiguous	Likely Benign	0.075	Likely Benign										-0.88	Neutral	0.454	Possibly Damaging	0.192	Benign	2.83	Benign	0.34	Tolerated	3.99	5	1	2	2.6	-18.03
c.2277G>C	M759I					6-33441742-G-C			-4.058	Likely Benign	0.393	Ambiguous	Likely Benign	0.075	Likely Benign										-0.88	Neutral	0.454	Possibly Damaging	0.192	Benign	2.83	Benign	0.34	Tolerated	3.99	5	1	2	2.6	-18.03
c.2279T>C	M760T					6-33441744-T-C	1	6.20e-7	-2.365	Likely Benign	0.519	Ambiguous	Likely Benign	0.096	Likely Benign										-1.56	Neutral	0.425	Benign	0.252	Benign	2.71	Benign	0.41	Tolerated	3.99	5	-1	-1	-2.6	-30.09
c.227C>G	S76C		Uncertain		1	6-33425835-C-G	2	1.24e-6	-5.408	Likely Benign	0.100	Likely Benign	Likely Benign	0.076	Likely Benign										-1.78	Neutral	0.992	Probably Damaging	0.869	Possibly Damaging	3.71	Benign	0.00	Affected	4.32	1	0	-1	3.3	16.06
c.227C>T	S76F					6-33425835-C-T	4	2.48e-6	-4.557	Likely Benign	0.197	Likely Benign	Likely Benign	0.082	Likely Benign										-2.40	Neutral	0.972	Probably Damaging	0.831	Possibly Damaging	3.71	Benign	0.00	Affected	4.32	1	-2	-3	3.6	60.10
c.2281C>T	R761W					6-33441746-C-T	1	6.20e-7	-9.248	Likely Pathogenic	0.665	Likely Pathogenic	Likely Benign	0.193	Likely Benign										-3.52	Deleterious	1.000	Probably Damaging	0.987	Probably Damaging	2.66	Benign	0.06	Tolerated	3.99	5	-3	2	3.6	30.03
c.2282G>A	R761Q		Uncertain		1	6-33441747-G-A	11	6.81e-6	-4.187	Likely Benign	0.202	Likely Benign	Likely Benign	0.191	Likely Benign										-0.63	Neutral	0.996	Probably Damaging	0.878	Possibly Damaging	2.75	Benign	0.40	Tolerated	3.99	5	1	1	1.0	-28.06
c.2282G>C	R761P		Uncertain		1	6-33441747-G-C	1	6.20e-7	-5.091	Likely Benign	0.640	Likely Pathogenic	Likely Benign	0.201	Likely Benign										-1.89	Neutral	0.999	Probably Damaging	0.968	Probably Damaging	2.69	Benign	0.38	Tolerated	3.99	5	0	-2	2.9	-59.07
c.2290A>C	N764H					6-33441755-A-C			-4.954	Likely Benign	0.320	Likely Benign	Likely Benign	0.091	Likely Benign										-2.09	Neutral	0.998	Probably Damaging	0.985	Probably Damaging	2.59	Benign	0.02	Affected	3.64	6	1	2	0.3	23.04
c.2291A>G	N764S		Benign		1				-3.149	Likely Benign	0.159	Likely Benign	Likely Benign	0.058	Likely Benign										-0.84	Neutral	0.992	Probably Damaging	0.846	Possibly Damaging	2.65	Benign	0.61	Tolerated	3.64	6	1	1	2.7	-27.03
c.2294G>A	S765N		Uncertain		1				-5.098	Likely Benign	0.378	Ambiguous	Likely Benign	0.094	Likely Benign										-0.94	Neutral	0.985	Probably Damaging	0.950	Probably Damaging	4.11	Benign	0.06	Tolerated	3.64	6	1	1	-2.7	27.03
c.2295C>A	S765R					6-33442453-C-A			-5.422	Likely Benign	0.791	Likely Pathogenic	Ambiguous	0.155	Likely Benign										-1.57	Neutral	0.996	Probably Damaging	0.985	Probably Damaging	4.16	Benign	0.07	Tolerated	3.64	6	-1	0	-3.7	69.11
c.2296T>C	S766P					6-33442454-T-C	1	1.28e-6	-7.343	In-Between	0.373	Ambiguous	Likely Benign	0.193	Likely Benign										-0.91	Neutral	0.006	Benign	0.013	Benign	4.07	Benign	0.01	Affected	3.64	6	-1	1	-0.8	10.04
c.2297C>A	S766Y					6-33442455-C-A			-8.636	Likely Pathogenic	0.641	Likely Pathogenic	Likely Benign	0.222	Likely Benign										-2.67	Deleterious	0.990	Probably Damaging	0.856	Possibly Damaging	4.09	Benign	0.00	Affected	3.64	6	-2	-3	-0.5	76.10
c.2297C>T	S766F					6-33442455-C-T			-8.944	Likely Pathogenic	0.709	Likely Pathogenic	Likely Benign	0.233	Likely Benign										-2.87	Deleterious	0.990	Probably Damaging	0.856	Possibly Damaging	4.08	Benign	0.00	Affected	3.64	6	-2	-3	3.6	60.10
c.2299A>G	I767V		Uncertain		1				-2.791	Likely Benign	0.064	Likely Benign	Likely Benign	0.096	Likely Benign										0.10	Neutral	0.072	Benign	0.029	Benign	4.21	Benign	1.00	Tolerated	3.64	6	4	3	-0.3	-14.03
c.229A>G	S77G					6-33425837-A-G	2	1.24e-6	-3.571	Likely Benign	0.064	Likely Benign	Likely Benign	0.014	Likely Benign										-1.23	Neutral	0.022	Benign	0.003	Benign	4.09	Benign	0.00	Affected	4.32	1	0	1	0.4	-30.03
c.2300T>C	I767T		Uncertain		1				-3.749	Likely Benign	0.252	Likely Benign	Likely Benign	0.138	Likely Benign										-0.78	Neutral	0.625	Possibly Damaging	0.249	Benign	4.12	Benign	0.46	Tolerated	3.64	6	0	-1	-5.2	-12.05
c.2302G>A	D768N					6-33442460-G-A	2	2.57e-6	-6.892	Likely Benign	0.453	Ambiguous	Likely Benign	0.048	Likely Benign										-0.77	Neutral	0.106	Benign	0.009	Benign	4.07	Benign	0.96	Tolerated	3.64	6	1	2	0.0	-0.98
c.2302G>T	D768Y		Uncertain		1	6-33442460-G-T			-9.866	Likely Pathogenic	0.824	Likely Pathogenic	Ambiguous	0.234	Likely Benign										-2.86	Deleterious	0.989	Probably Damaging	0.806	Possibly Damaging	4.01	Benign	0.07	Tolerated	3.64	6	-4	-3	2.2	48.09
c.2303A>C	D768A					6-33442461-A-C			-8.153	Likely Pathogenic	0.786	Likely Pathogenic	Ambiguous	0.174	Likely Benign										-1.84	Neutral	0.245	Benign	0.096	Benign	4.09	Benign	0.14	Tolerated	3.64	6	-2	0	5.3	-44.01
c.2305C>A	L769I					6-33442463-C-A			-3.993	Likely Benign	0.110	Likely Benign	Likely Benign	0.099	Likely Benign										-0.15	Neutral	0.836	Possibly Damaging	0.329	Benign	4.09	Benign	0.04	Affected	3.64	6	2	2	0.7	0.00
c.2314T>C	F772L					6-33442472-T-C	1	1.28e-6	-1.751	Likely Benign	0.762	Likely Pathogenic	Likely Benign	0.161	Likely Benign										-0.47	Neutral	0.508	Possibly Damaging	0.786	Possibly Damaging	4.31	Benign	1.00	Tolerated	3.64	6	0	2	1.0	-34.02
c.2316C>A	F772L					6-33442474-C-A			-1.751	Likely Benign	0.762	Likely Pathogenic	Likely Benign	0.109	Likely Benign										-0.47	Neutral	0.508	Possibly Damaging	0.786	Possibly Damaging	4.31	Benign	1.00	Tolerated	3.64	6	0	2	1.0	-34.02
c.2318T>C	M773T					6-33442476-T-C	1	1.28e-6	-4.225	Likely Benign	0.377	Ambiguous	Likely Benign	0.112	Likely Benign										-1.63	Neutral	0.106	Benign	0.471	Possibly Damaging	4.22	Benign	0.06	Tolerated	3.64	6	-1	-1	-2.6	-30.09
c.2318T>G	M773R					6-33442476-T-G	1	1.28e-6	-4.340	Likely Benign	0.597	Likely Pathogenic	Likely Benign	0.183	Likely Benign										-1.87	Neutral	0.220	Benign	0.471	Possibly Damaging	4.18	Benign	0.02	Affected	3.64	6	-1	0	-6.4	24.99
c.2321C>T	A774V					6-33442479-C-T	1	1.28e-6	-3.075	Likely Benign	0.108	Likely Benign	Likely Benign	0.055	Likely Benign										-0.73	Neutral	0.000	Benign	0.003	Benign	4.20	Benign	1.00	Tolerated	3.64	6	0	0	2.4	28.05
c.2324G>A	R775Q		Conflicting		3	6-33442482-G-A	11	1.41e-5	-4.476	Likely Benign	0.229	Likely Benign	Likely Benign	0.085	Likely Benign										-0.63	Neutral	0.969	Probably Damaging	0.863	Possibly Damaging	4.17	Benign	0.16	Tolerated	3.64	6	1	1	1.0	-28.06																10.1016/j.ajhg.2020.11.011
c.2324G>C	R775P		Benign		1				-5.072	Likely Benign	0.452	Ambiguous	Likely Benign	0.168	Likely Benign										-0.79	Neutral	0.971	Probably Damaging	0.944	Probably Damaging	4.13	Benign	0.07	Tolerated	3.64	6	-2	0	2.9	-59.07
c.2324G>T	R775L					6-33442482-G-T			-5.951	Likely Benign	0.598	Likely Pathogenic	Likely Benign	0.124	Likely Benign										-1.86	Neutral	0.933	Possibly Damaging	0.871	Possibly Damaging	4.13	Benign	0.06	Tolerated	3.64	6	-2	-3	8.3	-43.03
c.2326G>A	G776S					6-33442484-G-A	1	1.28e-6	-3.334	Likely Benign	0.147	Likely Benign	Likely Benign	0.163	Likely Benign										-1.21	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	4.28	Benign	0.13	Tolerated	3.64	6	0	1	-0.4	30.03
c.2326G>T	G776C					6-33442484-G-T			-7.974	In-Between	0.380	Ambiguous	Likely Benign	0.181	Likely Benign										-2.59	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	4.15	Benign	0.01	Affected	3.64	6	-3	-3	2.9	46.09
c.2327G>A	G776D					6-33442485-G-A			0.388	Likely Benign	0.566	Likely Pathogenic	Likely Benign	0.188	Likely Benign										0.16	Neutral	0.999	Probably Damaging	0.996	Probably Damaging	4.30	Benign	0.10	Tolerated	3.64	6	-1	1	-3.1	58.04
c.2327G>T	G776V					6-33442485-G-T			-6.541	Likely Benign	0.515	Ambiguous	Likely Benign	0.180	Likely Benign										-2.25	Neutral	0.999	Probably Damaging	0.998	Probably Damaging	4.19	Benign	0.01	Affected	3.64	6	-3	-1	4.6	42.08
c.2329C>A	L777I					6-33442487-C-A			-5.346	Likely Benign	0.128	Likely Benign	Likely Benign	0.096	Likely Benign										-0.85	Neutral	0.843	Possibly Damaging	0.920	Probably Damaging	4.05	Benign	0.02	Affected	3.64	6	2	2	0.7	0.00
c.2330T>C	L777P					6-33442488-T-C			-5.807	Likely Benign	0.361	Ambiguous	Likely Benign	0.255	Likely Benign										-2.13	Neutral	0.991	Probably Damaging	0.985	Probably Damaging	3.94	Benign	0.00	Affected	3.64	6	-3	-3	-5.4	-16.04
c.2333A>G	N778S					6-33442491-A-G	1	1.28e-6	-2.711	Likely Benign	0.097	Likely Benign	Likely Benign	0.137	Likely Benign										-0.61	Neutral	0.843	Possibly Damaging	0.893	Possibly Damaging	4.32	Benign	0.86	Tolerated	3.64	6	1	1	2.7	-27.03
c.2333A>T	N778I					6-33442491-A-T			-6.659	Likely Benign	0.622	Likely Pathogenic	Likely Benign	0.150	Likely Benign										-2.48	Neutral	0.991	Probably Damaging	0.980	Probably Damaging	4.17	Benign	0.02	Affected	3.64	6	-3	-2	8.0	-0.94
c.2334C>A	N778K					6-33442492-C-A			-6.768	Likely Benign	0.798	Likely Pathogenic	Ambiguous	0.113	Likely Benign										-1.57	Neutral	0.925	Possibly Damaging	0.932	Probably Damaging	4.27	Benign	0.18	Tolerated	3.64	6	0	1	-0.4	14.07
c.2336G>A	S779N					6-33442494-G-A			-4.880	Likely Benign	0.384	Ambiguous	Likely Benign	0.087	Likely Benign										-0.75	Neutral	0.021	Benign	0.026	Benign	2.30	Pathogenic	0.23	Tolerated	3.64	6	1	1	-2.7	27.03
c.2338T>C	S780P					6-33442890-T-C	1	6.22e-7	-6.055	Likely Benign	0.234	Likely Benign	Likely Benign	0.088	Likely Benign										-1.11	Neutral	0.995	Probably Damaging	0.892	Possibly Damaging	2.64	Benign	0.30	Tolerated	3.64	6	-1	1	-0.8	10.04
c.2339C>G	S780C		Uncertain		3	6-33442891-C-G	16	9.94e-6	-7.603	In-Between	0.278	Likely Benign	Likely Benign	0.078	Likely Benign										-1.41	Neutral	0.065	Benign	0.043	Benign	2.59	Benign	0.10	Tolerated	3.64	6	-1	0	3.3	16.06
c.233G>T	R78L		Uncertain		1				-3.389	Likely Benign	0.635	Likely Pathogenic	Likely Benign	0.062	Likely Benign										-1.59	Neutral	0.385	Benign	0.021	Benign	3.84	Benign	0.00	Affected			-3	-2	8.3	-43.03
c.2341A>G	M781V					6-33442893-A-G	4	2.48e-6	-2.624	Likely Benign	0.068	Likely Benign	Likely Benign	0.174	Likely Benign										0.00	Neutral	0.000	Benign	0.001	Benign	3.03	Benign	0.90	Tolerated	3.64	6	1	2	2.3	-32.06
c.2342T>C	M781T					6-33442894-T-C	1	6.21e-7	-3.774	Likely Benign	0.310	Likely Benign	Likely Benign	0.175	Likely Benign										-0.86	Neutral	0.015	Benign	0.037	Benign	2.75	Benign	0.59	Tolerated	3.64	6	-1	-1	-2.6	-30.09
c.2343G>A	M781I		Uncertain		1				-2.484	Likely Benign	0.323	Likely Benign	Likely Benign	0.101	Likely Benign										0.05	Neutral	0.000	Benign	0.001	Benign	2.89	Benign	1.00	Tolerated	3.64	6	1	2	2.6	-18.03
c.2343G>C	M781I					6-33442895-G-C	1	6.21e-7	-2.484	Likely Benign	0.323	Likely Benign	Likely Benign	0.101	Likely Benign										0.05	Neutral	0.000	Benign	0.001	Benign	2.89	Benign	1.00	Tolerated	3.64	6	1	2	2.6	-18.03
c.2347A>G	M783V					6-33442899-A-G	1	6.21e-7	-3.453	Likely Benign	0.086	Likely Benign	Likely Benign	0.065	Likely Benign										-0.96	Neutral	0.072	Benign	0.026	Benign	2.85	Benign	0.12	Tolerated	3.64	6	1	2	2.3	-32.06
c.2349G>A	M783I					6-33442901-G-A	6	3.72e-6	-3.560	Likely Benign	0.417	Ambiguous	Likely Benign	0.042	Likely Benign										-0.54	Neutral	0.004	Benign	0.006	Benign	2.87	Benign	0.22	Tolerated	3.64	6	1	2	2.6	-18.03
c.2350G>A	A784T		Benign		1				-3.579	Likely Benign	0.089	Likely Benign	Likely Benign	0.046	Likely Benign										1.23	Neutral	0.001	Benign	0.006	Benign	2.92	Benign	1.00	Tolerated	3.64	6	1	0	-2.5	30.03
c.2350G>C	A784P					6-33442902-G-C	4	2.48e-6	-3.777	Likely Benign	0.154	Likely Benign	Likely Benign	0.189	Likely Benign										-0.73	Neutral	0.586	Possibly Damaging	0.396	Benign	2.66	Benign	0.19	Tolerated	3.64	6	-1	1	-3.4	26.04
c.2351C>G	A784G					6-33442903-C-G	1	6.20e-7	-3.370	Likely Benign	0.158	Likely Benign	Likely Benign	0.056	Likely Benign										-1.24	Neutral	0.224	Benign	0.138	Benign	2.67	Benign	0.26	Tolerated	3.64	6	0	1	-2.2	-14.03
c.2353C>T	R785C	SH3-binding motif	Uncertain		1	6-33442905-C-T	29	1.80e-5	-5.887	Likely Benign	0.662	Likely Pathogenic	Likely Benign	0.126	Likely Benign										-5.06	Deleterious	0.144	Benign	0.046	Benign	2.22	Pathogenic	0.00	Affected	3.64	6	-4	-3	7.0	-53.05
c.2354G>A	R785H	SH3-binding motif	Uncertain		2	6-33442906-G-A	4	2.50e-6	-4.782	Likely Benign	0.388	Ambiguous	Likely Benign	0.129	Likely Benign										-2.61	Deleterious	0.999	Probably Damaging	0.947	Probably Damaging	2.25	Pathogenic	0.01	Affected	3.64	6	2	0	1.3	-19.05
c.2354G>C	R785P	SH3-binding motif				6-33442906-G-C			-3.603	Likely Benign	0.721	Likely Pathogenic	Likely Benign	0.203	Likely Benign										-4.12	Deleterious	0.998	Probably Damaging	0.958	Probably Damaging	2.24	Pathogenic	0.01	Affected	3.64	6	-2	0	2.9	-59.07
c.2357T>C	L786P	SH3-binding motif				6-33442909-T-C			-3.217	Likely Benign	0.656	Likely Pathogenic	Likely Benign	0.219	Likely Benign										-4.06	Deleterious	0.999	Probably Damaging	0.999	Probably Damaging	1.79	Pathogenic	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.2359C>A	P787T	SH3-binding motif	Likely Benign		1	6-33442911-C-A	17	1.05e-5	-4.813	Likely Benign	0.603	Likely Pathogenic	Likely Benign	0.258	Likely Benign										-4.40	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.46	Pathogenic	0.01	Affected	3.64	6	0	-1	0.9	3.99
c.2359C>T	P787S	SH3-binding motif	Uncertain		1	6-33442911-C-T	3	1.86e-6	-4.203	Likely Benign	0.564	Ambiguous	Likely Benign	0.221	Likely Benign										-3.81	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.48	Pathogenic	0.02	Affected	3.64	6	-1	1	0.8	-10.04
c.2362T>A	S788T	SH3-binding motif	Uncertain		2	6-33442914-T-A	4	2.49e-6	-4.288	Likely Benign	0.288	Likely Benign	Likely Benign	0.092	Likely Benign										-2.25	Neutral	0.979	Probably Damaging	0.982	Probably Damaging	1.55	Pathogenic	0.02	Affected	3.64	6	1	1	0.1	14.03
c.2362T>C	S788P	SH3-binding motif				6-33442914-T-C			-1.857	Likely Benign	0.435	Ambiguous	Likely Benign	0.236	Likely Benign										-3.91	Deleterious	0.997	Probably Damaging	0.995	Probably Damaging	1.51	Pathogenic	0.01	Affected	3.64	6	-1	1	-0.8	10.04
c.2368A>C	T790P	SH3-binding motif				6-33442920-A-C			-3.564	Likely Benign	0.088	Likely Benign	Likely Benign	0.250	Likely Benign										-3.55	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	2.25	Pathogenic	0.01	Affected	3.64	6	-1	0	-0.9	-3.99
c.2369C>A	T790N	SH3-binding motif	Conflicting		3	6-33442921-C-A	69	4.28e-5	-5.243	Likely Benign	0.276	Likely Benign	Likely Benign	0.103	Likely Benign										-2.54	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	2.27	Pathogenic	0.02	Affected	3.64	6	0	0	-2.8	13.00
c.2369C>G	T790S	SH3-binding motif	Uncertain		1				-3.914	Likely Benign	0.123	Likely Benign	Likely Benign	0.134	Likely Benign										-1.83	Neutral	0.997	Probably Damaging	0.989	Probably Damaging	2.39	Pathogenic	0.33	Tolerated	3.64	6	1	1	-0.1	-14.03
c.2372A>C	K791T	SH3-binding motif				6-33442924-A-C	2	1.24e-6	-1.578	Likely Benign	0.414	Ambiguous	Likely Benign	0.033	Likely Benign										-0.92	Neutral	0.032	Benign	0.017	Benign	4.17	Benign	0.16	Tolerated	3.64	6	-1	0	3.2	-27.07
c.2375A>C	E792A	SH3-binding motif				6-33442927-A-C	1	6.20e-7	-3.248	Likely Benign	0.514	Ambiguous	Likely Benign	0.060	Likely Benign										-3.35	Deleterious	0.000	Benign	0.001	Benign	3.92	Benign	0.01	Affected	3.64	6	-1	0	5.3	-58.04
c.2377A>G	K793E	SH3-binding motif				6-33442929-A-G			-4.233	Likely Benign	0.554	Ambiguous	Likely Benign	0.035	Likely Benign										-1.05	Neutral	0.001	Benign	0.006	Benign	4.17	Benign	0.05	Affected	4.07	3	1	0	0.4	0.94
c.2379G>C	K793N	SH3-binding motif				6-33442931-G-C	4	2.48e-6	-5.162	Likely Benign	0.632	Likely Pathogenic	Likely Benign	0.040	Likely Benign										1.18	Neutral	0.174	Benign	0.135	Benign	4.13	Benign	0.47	Tolerated	4.07	3	0	1	0.4	-14.07
c.237C>A	N79K					6-33425845-C-A	1	6.20e-7	-2.811	Likely Benign	0.422	Ambiguous	Likely Benign	0.030	Likely Benign										-0.91	Neutral	0.001	Benign	0.000	Benign	4.22	Benign	0.00	Affected	4.32	1	0	1	-0.4	14.07
c.237C>G	N79K					6-33425845-C-G	1	6.20e-7	-2.811	Likely Benign	0.422	Ambiguous	Likely Benign	0.030	Likely Benign										-0.91	Neutral	0.001	Benign	0.000	Benign	4.22	Benign	0.00	Affected	4.32	1	0	1	-0.4	14.07
c.2380C>A	P794T	SH3-binding motif				6-33442932-C-A	1	6.20e-7	-4.838	Likely Benign	0.060	Likely Benign	Likely Benign	0.046	Likely Benign										-0.34	Neutral	0.245	Benign	0.138	Benign	4.25	Benign	0.66	Tolerated	4.07	3	-1	0	0.9	3.99
c.2381C>T	P794L	SH3-binding motif	Benign/Likely benign		2	6-33442933-C-T	73	4.52e-5	-3.808	Likely Benign	0.079	Likely Benign	Likely Benign	0.075	Likely Benign										-0.80	Neutral	0.761	Possibly Damaging	0.321	Benign	4.24	Benign	0.03	Affected	4.07	3	-3	-3	5.4	16.04
c.2383C>T	P795S	SH3-binding motif				6-33442935-C-T	1	6.20e-7	-5.846	Likely Benign	0.067	Likely Benign	Likely Benign	0.056	Likely Benign										-0.23	Neutral	0.001	Benign	0.002	Benign	4.30	Benign	0.24	Tolerated	4.32	2	-1	1	0.8	-10.04
c.2386C>G	P796A	SH3-binding motif				6-33442938-C-G			-6.077	Likely Benign	0.050	Likely Benign	Likely Benign	0.023	Likely Benign										-0.31	Neutral	0.174	Benign	0.063	Benign	4.28	Benign	0.08	Tolerated	4.32	2	-1	1	3.4	-26.04
c.2393C>T	P798L	SH3-binding motif	Uncertain		2	6-33442945-C-T	6	3.72e-6	-5.640	Likely Benign	0.074	Likely Benign	Likely Benign	0.042	Likely Benign										-0.86	Neutral	0.981	Probably Damaging	0.631	Possibly Damaging	4.21	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.2399G>A	G800D	SH3-binding motif				6-33442951-G-A			-5.929	Likely Benign	0.400	Ambiguous	Likely Benign	0.088	Likely Benign										-0.84	Neutral	0.451	Benign	0.265	Benign	2.76	Benign	0.34	Tolerated	4.32	2	-1	1	-3.1	58.04
c.2399G>C	G800A	SH3-binding motif				6-33442951-G-C	7	4.34e-6	-3.550	Likely Benign	0.081	Likely Benign	Likely Benign	0.031	Likely Benign										-0.48	Neutral	0.011	Benign	0.006	Benign	2.78	Benign	1.00	Tolerated	4.32	2	0	1	2.2	14.03																10.1016/j.ajhg.2020.11.011
c.239A>G	K80R					6-33425847-A-G	1	6.20e-7	-2.919	Likely Benign	0.146	Likely Benign	Likely Benign	0.077	Likely Benign										0.11	Neutral	0.001	Benign	0.001	Benign	4.33	Benign	0.00	Affected	4.32	1	2	3	-0.6	28.01
c.23T>C	I8T					6-33420287-T-C			-3.149	Likely Benign	0.239	Likely Benign	Likely Benign	0.108	Likely Benign										-0.10	Neutral	0.047	Benign	0.006	Benign	4.03	Benign	0.00	Affected	4.32	1	-1	0	-5.2	-12.05
c.2401G>A	G801S	SH3-binding motif	Uncertain		1				-3.665	Likely Benign	0.087	Likely Benign	Likely Benign	0.039	Likely Benign										-0.41	Neutral	0.009	Benign	0.019	Benign	2.76	Benign	0.48	Tolerated	4.32	2	0	1	-0.4	30.03
c.2404G>A	G802S	SH3-binding motif				6-33442956-G-A	1	6.20e-7	-2.663	Likely Benign	0.078	Likely Benign	Likely Benign	0.098	Likely Benign										0.32	Neutral	0.001	Benign	0.006	Benign	2.83	Benign	0.06	Tolerated	3.77	5	0	1	-0.4	30.03
c.2405G>A	G802D	SH3-binding motif	Uncertain		1	6-33442957-G-A	1	6.20e-7	-5.083	Likely Benign	0.476	Ambiguous	Likely Benign	0.153	Likely Benign										-0.38	Neutral	0.126	Benign	0.138	Benign	2.72	Benign	0.09	Tolerated	3.77	5	1	-1	-3.1	58.04
c.2408A>G	K803R	SH3-binding motif	Uncertain		1				-2.281	Likely Benign	0.097	Likely Benign	Likely Benign	0.018	Likely Benign										-1.52	Neutral	0.103	Benign	0.038	Benign	2.38	Pathogenic	0.00	Affected	3.77	5	3	2	-0.6	28.01
c.2411A>C	D804A	SH3-binding motif				6-33442963-A-C			-6.086	Likely Benign	0.758	Likely Pathogenic	Likely Benign	0.269	Likely Benign										-3.99	Deleterious	0.980	Probably Damaging	0.858	Possibly Damaging	1.21	Pathogenic	0.04	Affected	3.77	5	-2	0	5.3	-44.01
c.2411A>G	D804G	SH3-binding motif				6-33442963-A-G	1	6.20e-7	-5.051	Likely Benign	0.680	Likely Pathogenic	Likely Benign	0.287	Likely Benign										-3.82	Deleterious	0.980	Probably Damaging	0.858	Possibly Damaging	1.21	Pathogenic	0.04	Affected	3.77	5	-1	1	3.1	-58.04
c.2414T>C	L805P	SH3-binding motif	Uncertain		1				-4.661	Likely Benign	0.444	Ambiguous	Likely Benign	0.272	Likely Benign										-3.40	Deleterious	0.975	Probably Damaging	0.767	Possibly Damaging	2.36	Pathogenic	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.2417T>C	F806S	SH3-binding motif				6-33442969-T-C	1	6.20e-7	-6.959	Likely Benign	0.911	Likely Pathogenic	Ambiguous	0.269	Likely Benign										-4.13	Deleterious	0.999	Probably Damaging	0.996	Probably Damaging	2.21	Pathogenic	0.00	Affected	3.77	5	-2	-3	-3.6	-60.10
c.241C>A	L81M					6-33425849-C-A	1	6.20e-7	-5.351	Likely Benign	0.254	Likely Benign	Likely Benign	0.039	Likely Benign										-0.27	Neutral	0.789	Possibly Damaging	0.165	Benign	3.95	Benign	0.00	Affected	4.32	1	2	4	-1.9	18.03
c.2420A>G	Y807C	SH3-binding motif	Uncertain		1	6-33442972-A-G	1	6.20e-7	-7.228	In-Between	0.204	Likely Benign	Likely Benign	0.243	Likely Benign										-3.89	Deleterious	0.997	Probably Damaging	0.934	Probably Damaging	2.42	Pathogenic	0.01	Affected	3.77	5	0	-2	3.8	-60.04
c.2420A>T	Y807F	SH3-binding motif	Uncertain		1				-3.667	Likely Benign	0.073	Likely Benign	Likely Benign	0.057	Likely Benign										0.14	Neutral	0.012	Benign	0.022	Benign	2.92	Benign	0.98	Tolerated	3.77	5	7	3	4.1	-16.00
c.2428C>T	R810C	SH3-binding motif				6-33442980-C-T	2	1.24e-6	-8.925	Likely Pathogenic	0.839	Likely Pathogenic	Ambiguous	0.245	Likely Benign										-4.91	Deleterious	1.000	Probably Damaging	0.991	Probably Damaging	2.32	Pathogenic	0.00	Affected	3.77	5	-3	-4	7.0	-53.05
c.2429G>A	R810H	SH3-binding motif				6-33442981-G-A	3	1.86e-6	-6.554	Likely Benign	0.550	Ambiguous	Likely Benign	0.239	Likely Benign										-2.80	Deleterious	1.000	Probably Damaging	0.980	Probably Damaging	2.35	Pathogenic	0.01	Affected	3.77	5	0	2	1.3	-19.05
c.2434C>T	P812S	SH3-binding motif	Uncertain		1	6-33442986-C-T	1	6.20e-7	-5.689	Likely Benign	0.456	Ambiguous	Likely Benign	0.162	Likely Benign										-0.62	Neutral	0.999	Probably Damaging	0.966	Probably Damaging	2.89	Benign	0.95	Tolerated	4.32	4	1	-1	0.8	-10.04
c.2435C>A	P812H	SH3-binding motif	Uncertain		1	6-33442987-C-A	3	1.86e-6	-7.470	In-Between	0.698	Likely Pathogenic	Likely Benign	0.272	Likely Benign										-2.81	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	2.68	Benign	0.00	Affected	4.32	4	0	-2	-1.6	40.02
c.2435C>T	P812L	SH3-binding motif				6-33442987-C-T	1	6.20e-7	-7.121	In-Between	0.591	Likely Pathogenic	Likely Benign	0.172	Likely Benign										-2.61	Deleterious	0.978	Probably Damaging	0.824	Possibly Damaging	2.76	Benign	0.01	Affected	4.32	4	-3	-3	5.4	16.04
c.2443C>G	R815G	SH3-binding motif	Uncertain		1				-7.983	In-Between	0.854	Likely Pathogenic	Ambiguous	0.146	Likely Benign										-3.22	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	2.62	Benign	0.02	Affected	4.32	4	-3	-2	4.1	-99.14
c.2443C>T	R815C	SH3-binding motif	Uncertain		1	6-33442995-C-T	5	3.10e-6	-9.373	Likely Pathogenic	0.828	Likely Pathogenic	Ambiguous	0.174	Likely Benign										-3.89	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.59	Benign	0.00	Affected	4.32	4	-4	-3	7.0	-53.05
c.2444G>A	R815H	SH3-binding motif	Likely Benign		2	6-33442996-G-A	24	1.49e-5	-7.474	In-Between	0.553	Ambiguous	Likely Benign	0.157	Likely Benign										-1.81	Neutral	1.000	Probably Damaging	0.998	Probably Damaging	2.61	Benign	0.02	Affected	4.32	4	2	0	1.3	-19.05																10.1016/j.ajhg.2020.11.011
c.2444G>T	R815L		Uncertain		1				-8.546	Likely Pathogenic	0.865	Likely Pathogenic	Ambiguous	0.175	Likely Benign										-3.06	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	2.63	Benign	0.03	Affected	4.32	4	-2	-3	8.3	-43.03
c.244C>G	L82V					6-33425852-C-G			-6.701	Likely Benign	0.914	Likely Pathogenic	Ambiguous	0.065	Likely Benign										-1.13	Neutral	0.371	Benign	0.024	Benign	3.72	Benign	0.00	Affected	4.32	1	1	2	0.4	-14.03
c.2452C>T	P818S					6-33443004-C-T	1	6.20e-7	-5.740	Likely Benign	0.932	Likely Pathogenic	Ambiguous	0.203	Likely Benign										-4.38	Deleterious	0.989	Probably Damaging	0.824	Possibly Damaging	2.04	Pathogenic	0.04	Affected	3.77	5	-1	1	0.8	-10.04
c.2453C>T	P818L					6-33443005-C-T	1	6.20e-7	-6.064	Likely Benign	0.938	Likely Pathogenic	Ambiguous	0.285	Likely Benign										-5.81	Deleterious	0.997	Probably Damaging	0.954	Probably Damaging	1.98	Pathogenic	0.02	Affected	3.77	5	-3	-3	5.4	16.04
c.2456C>T	A819V					6-33443008-C-T	1	6.19e-7	-4.944	Likely Benign	0.797	Likely Pathogenic	Ambiguous	0.246	Likely Benign										-2.40	Neutral	0.998	Probably Damaging	0.963	Probably Damaging	2.19	Pathogenic	0.01	Affected	3.77	5	0	0	2.4	28.05
c.2458T>C	Y820H					6-33443010-T-C	5	3.10e-6	-7.432	In-Between	0.928	Likely Pathogenic	Ambiguous	0.129	Likely Benign										-0.13	Neutral	0.999	Probably Damaging	0.989	Probably Damaging	2.70	Benign	0.24	Tolerated	3.77	5	2	0	-1.9	-26.03
c.2459A>G	Y820C		Uncertain		1				-8.797	Likely Pathogenic	0.744	Likely Pathogenic	Likely Benign	0.113	Likely Benign										-3.16	Deleterious	1.000	Probably Damaging	0.983	Probably Damaging	2.68	Benign	0.06	Tolerated	3.77	5	0	-2	3.8	-60.04
c.245T>C	L82P					6-33425853-T-C	1	6.20e-7	-7.667	In-Between	0.991	Likely Pathogenic	Likely Pathogenic	0.125	Likely Benign										-2.73	Deleterious	0.939	Possibly Damaging	0.162	Benign	3.64	Benign	0.00	Affected	4.32	1	-3	-3	-5.4	-16.04
c.2465C>T	T822M					6-33443017-C-T	5	3.10e-6	-4.525	Likely Benign	0.833	Likely Pathogenic	Ambiguous	0.239	Likely Benign										-2.11	Neutral	1.000	Probably Damaging	0.989	Probably Damaging	2.48	Pathogenic	0.03	Affected	3.77	5	-1	-1	2.6	30.09
c.2470A>G	S824G					6-33443022-A-G	1	6.20e-7	-5.476	Likely Benign	0.543	Ambiguous	Likely Benign	0.079	Likely Benign										-1.74	Neutral	0.992	Probably Damaging	0.987	Probably Damaging	2.60	Benign	0.50	Tolerated	3.77	5	0	1	0.4	-30.03
c.2471G>A	S824N					6-33443023-G-A	2	1.24e-6	-4.473	Likely Benign	0.909	Likely Pathogenic	Ambiguous	0.091	Likely Benign										-1.08	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.67	Benign	0.61	Tolerated	3.77	5	1	1	-2.7	27.03
c.2474C>T	S825L					6-33443026-C-T	1	6.20e-7	-4.987	Likely Benign	0.910	Likely Pathogenic	Ambiguous	0.249	Likely Benign										-4.30	Deleterious	0.999	Probably Damaging	0.994	Probably Damaging	1.94	Pathogenic	0.01	Affected	3.77	5	-2	-3	4.6	26.08
c.2482A>G	T828A					6-33443034-A-G	1	6.20e-7	-2.974	Likely Benign	0.340	Likely Benign	Likely Benign	0.197	Likely Benign										-2.13	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.67	Benign	0.24	Tolerated	3.77	5	0	1	2.5	-30.03
c.2485G>A	E829K		Pathogenic		1				-7.527	In-Between	0.807	Likely Pathogenic	Ambiguous	0.194	Likely Benign										-2.65	Deleterious	0.994	Probably Damaging	0.900	Possibly Damaging	2.27	Pathogenic	0.00	Affected	3.77	5	0	1	-0.4	-0.94
c.2493G>C	E831D		Uncertain		1	6-33443045-G-C	1	6.19e-7	-3.055	Likely Benign	0.063	Likely Benign	Likely Benign	0.073	Likely Benign										1.23	Neutral	0.002	Benign	0.002	Benign	2.64	Benign	0.77	Tolerated	3.77	5	3	2	0.0	-14.03
c.249A>C	R83S					6-33425857-A-C	1	6.20e-7	-2.550	Likely Benign	0.999	Likely Pathogenic	Likely Pathogenic	0.094	Likely Benign										-1.87	Neutral	0.909	Possibly Damaging	0.587	Possibly Damaging	3.19	Benign	0.00	Affected	4.32	1	0	-1	3.7	-69.11
c.249A>T	R83S		Uncertain		1				-2.550	Likely Benign	0.999	Likely Pathogenic	Likely Pathogenic	0.094	Likely Benign										-1.87	Neutral	0.909	Possibly Damaging	0.587	Possibly Damaging	3.19	Benign	0.00	Affected	4.32	1	0	-1	3.7	-69.11
c.2502G>C	M834I		Uncertain		1				-3.377	Likely Benign	0.291	Likely Benign	Likely Benign	0.055	Likely Benign										-1.21	Neutral	0.026	Benign	0.009	Benign	2.56	Benign	0.00	Affected	4.32	4	1	2	2.6	-18.03
c.2503C>A	L835M		Uncertain		1				-4.153	Likely Benign	0.121	Likely Benign	Likely Benign	0.068	Likely Benign										-0.45	Neutral	0.999	Probably Damaging	0.977	Probably Damaging	2.67	Benign	0.12	Tolerated	3.77	5	2	4	-1.9	18.03
c.2503C>G	L835V					6-33443055-C-G	1	6.19e-7	-3.439	Likely Benign	0.115	Likely Benign	Likely Benign	0.073	Likely Benign										-0.70	Neutral	0.995	Probably Damaging	0.926	Probably Damaging	2.72	Benign	0.17	Tolerated	3.77	5	1	2	0.4	-14.03
c.2506A>G	S836G		Uncertain		1	6-33443058-A-G	4	2.48e-6	-4.749	Likely Benign	0.112	Likely Benign	Likely Benign	0.066	Likely Benign										-1.65	Neutral	0.006	Benign	0.019	Benign	2.54	Benign	0.39	Tolerated	3.77	5	1	0	0.4	-30.03
c.2509G>A	V837I					6-33443061-G-A	1	6.19e-7	-4.299	Likely Benign	0.119	Likely Benign	Likely Benign	0.119	Likely Benign										-0.51	Neutral	0.992	Probably Damaging	0.989	Probably Damaging	2.63	Benign	0.13	Tolerated	3.77	5	3	4	0.3	14.03
c.250C>G	R84G		Uncertain		1				-6.627	Likely Benign	0.989	Likely Pathogenic	Likely Pathogenic	0.139	Likely Benign										-2.64	Deleterious	0.962	Probably Damaging	0.726	Possibly Damaging	3.68	Benign	0.00	Affected	4.32	1	-3	-2	4.1	-99.14
c.2514C>A	N838K		Uncertain		2				-8.470	Likely Pathogenic	0.862	Likely Pathogenic	Ambiguous	0.097	Likely Benign										-2.78	Deleterious	0.997	Probably Damaging	0.995	Probably Damaging	2.69	Benign	0.16	Tolerated	3.77	5	1	0	-0.4	14.07
c.2516A>G	K839R					6-33443068-A-G	1	6.20e-7	-7.111	In-Between	0.162	Likely Benign	Likely Benign	0.133	Likely Benign										-0.88	Neutral	0.972	Probably Damaging	0.860	Possibly Damaging	2.72	Benign	0.31	Tolerated	3.77	5	2	3	-0.6	28.01
c.2518A>T	S840C		Uncertain		1				-8.799	Likely Pathogenic	0.904	Likely Pathogenic	Ambiguous	0.376	Likely Benign										-3.96	Deleterious	0.999	Probably Damaging	0.975	Probably Damaging	1.50	Pathogenic	0.00	Affected	3.77	5	0	-1	3.3	16.06
c.2521G>A	V841M		Uncertain		1	6-33443073-G-A	3	1.86e-6	-7.000	In-Between	0.651	Likely Pathogenic	Likely Benign	0.119	Likely Benign										-0.74	Neutral	0.999	Probably Damaging	0.998	Probably Damaging	2.54	Benign	0.02	Affected	3.77	5	1	2	-2.3	32.06
c.2522T>C	V841A		Uncertain		1	6-33443074-T-C	3	1.86e-6	-8.152	Likely Pathogenic	0.901	Likely Pathogenic	Ambiguous	0.183	Likely Benign										-2.13	Neutral	0.992	Probably Damaging	0.989	Probably Damaging	2.57	Benign	0.02	Affected	3.77	5	0	0	-2.4	-28.05
c.2525C>A	S842Y		Likely Pathogenic		1				-16.124	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.191	Likely Benign										-4.28	Deleterious	0.944	Possibly Damaging	0.676	Possibly Damaging	1.97	Pathogenic	0.00	Affected	3.77	5	-3	-2	-0.5	76.10
c.2529G>A	M843I					6-33443081-G-A	1	6.20e-7	-6.219	Likely Benign	0.983	Likely Pathogenic	Likely Pathogenic	0.209	Likely Benign										-1.97	Neutral	0.925	Possibly Damaging	0.954	Probably Damaging	2.66	Benign	0.03	Affected	3.77	5	1	2	2.6	-18.03
c.2543G>T	G848V					6-33443095-G-T	1	6.20e-7	-4.445	Likely Benign	0.255	Likely Benign	Likely Benign	0.218	Likely Benign										-1.39	Neutral	0.977	Probably Damaging	0.856	Possibly Damaging	2.57	Benign	0.02	Affected	4.32	4	-3	-1	4.6	42.08
c.2548G>A	G850R		Uncertain		1				-5.082	Likely Benign	0.398	Ambiguous	Likely Benign	0.194	Likely Benign										-0.07	Neutral	0.010	Benign	0.010	Benign	4.30	Benign	0.01	Affected	3.77	5	-3	-2	-4.1	99.14
c.2555G>A	G852D					6-33443107-G-A	1	6.20e-7	-5.588	Likely Benign	0.203	Likely Benign	Likely Benign	0.154	Likely Benign										0.67	Neutral	0.001	Benign	0.005	Benign	4.18	Benign	0.01	Affected	3.77	5	-1	1	-3.1	58.04
c.2557G>C	G853R		Uncertain		1				-4.749	Likely Benign	0.366	Ambiguous	Likely Benign	0.091	Likely Benign										-1.27	Neutral	0.846	Possibly Damaging	0.624	Possibly Damaging	4.18	Benign	0.00	Affected			-3	-2	-4.1	99.14
c.2560C>T	R854C		Uncertain		1	6-33443112-C-T	3	1.86e-6	-5.082	Likely Benign	0.170	Likely Benign	Likely Benign	0.174	Likely Benign										-2.48	Neutral	1.000	Probably Damaging	0.947	Probably Damaging	4.05	Benign	0.01	Affected	3.88	3	-3	-4	7.0	-53.05
c.2561G>A	R854H		Uncertain		1	6-33443113-G-A	4	2.48e-6	-3.686	Likely Benign	0.094	Likely Benign	Likely Benign	0.183	Likely Benign										-1.38	Neutral	0.997	Probably Damaging	0.899	Possibly Damaging	4.07	Benign	0.04	Affected	3.88	3	2	0	1.3	-19.05
c.2567A>G	N856S		Uncertain		1	6-33443119-A-G	2	1.24e-6	-2.104	Likely Benign	0.064	Likely Benign	Likely Benign	0.040	Likely Benign										-1.54	Neutral	0.901	Possibly Damaging	0.535	Possibly Damaging	4.16	Benign	0.30	Tolerated	3.88	3	1	1	2.7	-27.03
c.256G>A	V86I		Uncertain		1				-4.726	Likely Benign	0.338	Likely Benign	Likely Benign	0.076	Likely Benign										-0.31	Neutral	0.267	Benign	0.097	Benign	3.94	Benign	0.00	Affected	4.32	1	4	3	0.3	14.03
c.256G>C	V86L					6-33425864-G-C	1	6.20e-7	-3.658	Likely Benign	0.965	Likely Pathogenic	Likely Pathogenic	0.081	Likely Benign										-0.84	Neutral	0.267	Benign	0.097	Benign	3.85	Benign	0.00	Affected	4.32	1	1	2	-0.4	14.03
c.2573G>A	S858N		Uncertain		1	6-33443125-G-A	2	1.24e-6	-4.311	Likely Benign	0.121	Likely Benign	Likely Benign	0.107	Likely Benign										-0.67	Neutral	0.448	Benign	0.846	Possibly Damaging	4.13	Benign	0.02	Affected	3.77	5	1	1	-2.7	27.03
c.2578G>A	V860I		Benign		1	6-33443130-G-A	21	1.30e-5	-4.516	Likely Benign	0.095	Likely Benign	Likely Benign	0.039	Likely Benign										-0.42	Neutral	0.009	Benign	0.006	Benign	4.24	Benign	0.00	Affected	3.77	5	4	3	0.3	14.03
c.2582C>T	S861L		Uncertain		1	6-33443134-C-T	2	1.24e-6	-4.966	Likely Benign	0.219	Likely Benign	Likely Benign	0.144	Likely Benign										-2.10	Neutral	0.904	Possibly Damaging	0.355	Benign	3.93	Benign	0.07	Tolerated	4.32	3	-3	-2	4.6	26.08
c.2591C>T	A864V		Uncertain		2	6-33443143-C-T	6	3.72e-6	-4.749	Likely Benign	0.126	Likely Benign	Likely Benign	0.038	Likely Benign										-1.35	Neutral	0.767	Possibly Damaging	0.119	Benign	2.45	Pathogenic	0.30	Tolerated	3.82	4	0	0	2.4	28.05
c.2596G>A	V866I		Conflicting		3	6-33443148-G-A	5	3.10e-6	-4.652	Likely Benign	0.118	Likely Benign	Likely Benign	0.059	Likely Benign										-0.39	Neutral	0.957	Probably Damaging	0.541	Possibly Damaging	2.69	Benign	0.27	Tolerated	3.82	4	4	3	0.3	14.03
c.2596G>T	V866L		Uncertain		1	6-33443148-G-T	1	6.20e-7	-3.352	Likely Benign	0.148	Likely Benign	Likely Benign	0.046	Likely Benign										-0.97	Neutral	0.217	Benign	0.229	Benign	2.71	Benign	0.21	Tolerated	3.82	4	2	1	-0.4	14.03
c.2597T>C	V866A					6-33443149-T-C	1	6.20e-7	-1.805	Likely Benign	0.101	Likely Benign	Likely Benign	0.054	Likely Benign										-1.27	Neutral	0.889	Possibly Damaging	0.682	Possibly Damaging	2.87	Benign	0.37	Tolerated	3.82	4	0	0	-2.4	-28.05
c.2599G>C	G867R					6-33443151-G-C	1	6.20e-7	-3.569	Likely Benign	0.755	Likely Pathogenic	Likely Benign	0.131	Likely Benign										-1.76	Neutral	0.997	Probably Damaging	0.943	Probably Damaging	2.70	Benign	0.05	Affected	3.82	4	-2	-3	-4.1	99.14
c.25C>A	H9N					6-33420289-C-A			-3.789	Likely Benign	0.103	Likely Benign	Likely Benign	0.081	Likely Benign										-0.36	Neutral	0.024	Benign	0.003	Benign	4.23	Benign	0.00	Affected	4.32	1	1	2	-0.3	-23.04
c.25C>T	H9Y					6-33420289-C-T			-3.833	Likely Benign	0.136	Likely Benign	Likely Benign	0.082	Likely Benign										-0.14	Neutral	0.047	Benign	0.006	Benign	4.24	Benign	0.00	Affected	4.32	1	2	0	1.9	26.03
c.2600G>A	G867E					6-33443152-G-A	3	1.86e-6	-5.204	Likely Benign	0.492	Ambiguous	Likely Benign	0.105	Likely Benign										-1.57	Neutral	0.994	Probably Damaging	0.943	Probably Damaging	2.74	Benign	0.07	Tolerated	3.82	4	-2	0	-3.1	72.06
c.2602G>C	D868H					6-33443154-G-C	1	6.20e-7	-3.358	Likely Benign	0.763	Likely Pathogenic	Likely Benign	0.212	Likely Benign										-2.34	Neutral	1.000	Probably Damaging	0.983	Probably Damaging	2.49	Pathogenic	0.08	Tolerated	3.82	4	-1	1	0.3	22.05
c.2608C>G	L870V		Uncertain		1				-4.123	Likely Benign	0.300	Likely Benign	Likely Benign	0.111	Likely Benign										-1.19	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.64	Benign	0.12	Tolerated	3.88	3	2	1	0.4	-14.03
c.2613C>G	H871Q					6-33443165-C-G	1	6.20e-7	-4.049	Likely Benign	0.140	Likely Benign	Likely Benign	0.061	Likely Benign										-0.67	Neutral	0.255	Benign	0.113	Benign	2.69	Benign	0.17	Tolerated	3.88	3	0	3	-0.3	-9.01
c.2617A>G	S873G					6-33443169-A-G	4	2.48e-6	-5.702	Likely Benign	0.219	Likely Benign	Likely Benign	0.120	Likely Benign										-1.88	Neutral	0.979	Probably Damaging	0.982	Probably Damaging	2.68	Benign	0.75	Tolerated	3.77	5	0	1	0.4	-30.03
c.2619C>G	S873R		Uncertain		1	6-33443171-C-G	1	6.20e-7	-5.856	Likely Benign	0.976	Likely Pathogenic	Likely Pathogenic	0.192	Likely Benign										-2.74	Deleterious	0.997	Probably Damaging	0.995	Probably Damaging	2.67	Benign	0.06	Tolerated	3.77	5	0	-1	-3.7	69.11
c.2621A>C	Q874P					6-33443173-A-C	9	5.58e-6	-4.622	Likely Benign	0.125	Likely Benign	Likely Benign	0.219	Likely Benign										-2.89	Deleterious	0.996	Probably Damaging	0.992	Probably Damaging	2.77	Benign	0.00	Affected	3.77	5	-1	0	1.9	-31.01
c.2623G>A	A875T					6-33443175-G-A	1	6.20e-7	-3.793	Likely Benign	0.179	Likely Benign	Likely Benign	0.110	Likely Benign										-1.56	Neutral	0.972	Probably Damaging	0.864	Possibly Damaging	2.72	Benign	0.26	Tolerated	3.77	5	0	1	-2.5	30.03
c.2627C>G	S876W					6-33443179-C-G	1	6.20e-7	-9.305	Likely Pathogenic	0.829	Likely Pathogenic	Ambiguous	0.291	Likely Benign										-3.72	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.54	Benign	0.01	Affected	3.77	5	-3	-2	-0.1	99.14
c.2627C>T	S876L		Uncertain		2				-5.856	Likely Benign	0.489	Ambiguous	Likely Benign	0.249	Likely Benign										-3.56	Deleterious	0.998	Probably Damaging	0.992	Probably Damaging	2.57	Benign	0.05	Affected	3.77	5	-2	-3	4.6	26.08
c.2632A>G	T878A		Uncertain		1				-2.154	Likely Benign	0.081	Likely Benign	Likely Benign	0.088	Likely Benign										-0.67	Neutral	0.003	Benign	0.006	Benign	2.73	Benign	0.18	Tolerated	3.77	5	1	0	2.5	-30.03
c.2635G>A	A879T					6-33443187-G-A	3	1.86e-6	-5.161	Likely Benign	0.090	Likely Benign	Likely Benign	0.042	Likely Benign										-0.98	Neutral	0.872	Possibly Damaging	0.580	Possibly Damaging	2.66	Benign	0.19	Tolerated	3.77	5	0	1	-2.5	30.03
c.2635_2636delinsAA	A879K		Likely Benign		1				-5.877	Likely Benign	0.757	Likely Pathogenic	Likely Benign												-0.71	Neutral	0.969	Probably Damaging	0.593	Possibly Damaging	2.69	Benign	0.21	Tolerated	3.77	5	-1	-1	-5.7	57.10
c.2636C>A	A879E					6-33443188-C-A	1	6.20e-7	-3.786	Likely Benign	0.503	Ambiguous	Likely Benign	0.070	Likely Benign										-0.27	Neutral	0.872	Possibly Damaging	0.659	Possibly Damaging	2.70	Benign	0.27	Tolerated	3.77	5	-1	0	-5.3	58.04
c.2636C>G	A879G					6-33443188-C-G	1	6.20e-7	-3.924	Likely Benign	0.085	Likely Benign	Likely Benign	0.054	Likely Benign										-0.43	Neutral	0.001	Benign	0.007	Benign	2.69	Benign	0.43	Tolerated	3.77	5	0	1	-2.2	-14.03
c.2639C>G	A880G					6-33443191-C-G	2	1.24e-6	-3.283	Likely Benign	0.071	Likely Benign	Likely Benign	0.049	Likely Benign										-0.14	Neutral	0.002	Benign	0.007	Benign	2.62	Benign	0.04	Affected	3.77	5	0	1	-2.2	-14.03
c.2639C>T	A880V					6-33443191-C-T	1	6.20e-7	-5.440	Likely Benign	0.120	Likely Benign	Likely Benign	0.095	Likely Benign										-0.11	Neutral	0.761	Possibly Damaging	0.399	Benign	2.58	Benign	1.00	Tolerated	3.77	5	0	0	2.4	28.05
c.263T>C	V88A		Uncertain		1				-5.860	Likely Benign	0.993	Likely Pathogenic	Likely Pathogenic	0.050	Likely Benign										-1.22	Neutral	0.053	Benign	0.008	Benign	3.75	Benign	0.00	Affected	4.32	1	0	0	-2.4	-28.05
c.2648T>A	L883Q					6-33443200-T-A	3	1.86e-6	-3.559	Likely Benign	0.123	Likely Benign	Likely Benign	0.129	Likely Benign										-0.51	Neutral	0.934	Possibly Damaging	0.637	Possibly Damaging	2.66	Benign	0.11	Tolerated	4.32	4	-2	-2	-7.3	14.97
c.2650C>T	R884W		Uncertain		1	6-33443202-C-T	5	3.10e-6	-3.785	Likely Benign	0.332	Likely Benign	Likely Benign	0.151	Likely Benign										0.26	Neutral	0.995	Probably Damaging	0.812	Possibly Damaging	2.56	Benign	0.05	Affected	4.32	4	-3	2	3.6	30.03
c.2651G>A	R884Q		Uncertain		2	6-33443203-G-A	5	3.10e-6	-3.785	Likely Benign	0.128	Likely Benign	Likely Benign	0.055	Likely Benign										-0.42	Neutral	0.012	Benign	0.004	Benign	2.62	Benign	0.36	Tolerated	4.32	4	1	1	1.0	-28.06
c.2654C>G	P885R					6-33443206-C-G	1	6.20e-7	-4.166	Likely Benign	0.307	Likely Benign	Likely Benign	0.072	Likely Benign										-1.99	Neutral	0.586	Possibly Damaging	0.377	Benign	2.84	Benign	0.00	Affected	4.32	4	-2	0	-2.9	59.07
c.2657C>T	A886V		Uncertain		1	6-33443209-C-T	18	1.12e-5	-4.478	Likely Benign	0.078	Likely Benign	Likely Benign	0.061	Likely Benign										-0.20	Neutral	0.888	Possibly Damaging	0.314	Benign	2.17	Pathogenic	0.00	Affected	4.32	4	0	0	2.4	28.05
c.265C>G	P89A		Uncertain		2				-5.778	Likely Benign	0.920	Likely Pathogenic	Ambiguous	0.095	Likely Benign										-2.47	Neutral	0.225	Benign	0.020	Benign	3.77	Benign	0.00	Affected	4.32	1	1	-1	3.4	-26.04
c.2662G>A	A888T					6-33443214-G-A	1	6.20e-7	-4.792	Likely Benign	0.084	Likely Benign	Likely Benign	0.059	Likely Benign										-1.11	Neutral	0.001	Benign	0.002	Benign	2.62	Benign	0.00	Affected	4.32	4	0	1	-2.5	30.03
c.2662G>C	A888P					6-33443214-G-C	5	3.10e-6	-2.368	Likely Benign	0.083	Likely Benign	Likely Benign	0.050	Likely Benign										-0.02	Neutral	0.000	Benign	0.000	Benign	2.56	Benign	0.00	Affected	4.32	4	-1	1	-3.4	26.04
c.2663C>G	A888G					6-33443215-C-G	5	3.10e-6	-2.523	Likely Benign	0.073	Likely Benign	Likely Benign	0.047	Likely Benign										-0.32	Neutral	0.033	Benign	0.036	Benign	2.69	Benign	0.00	Affected	4.32	4	0	1	-2.2	-14.03																10.1016/j.ajhg.2020.11.011
c.2663C>T	A888V					6-33443215-C-T	1	6.20e-7	-4.241	Likely Benign	0.106	Likely Benign	Likely Benign	0.034	Likely Benign										-0.91	Neutral	0.000	Benign	0.001	Benign	2.78	Benign	0.00	Affected	4.32	4	0	0	2.4	28.05
c.2665G>A	G889R					6-33443217-G-A	1	6.20e-7	-3.357	Likely Benign	0.684	Likely Pathogenic	Likely Benign	0.070	Likely Benign										-1.96	Neutral	0.027	Benign	0.009	Benign	2.38	Pathogenic	0.02	Affected	4.32	4	-2	-3	-4.1	99.14
c.2666G>C	G889A					6-33443218-G-C	1	6.20e-7	-4.580	Likely Benign	0.099	Likely Benign	Likely Benign	0.063	Likely Benign										-1.49	Neutral	0.245	Benign	0.096	Benign	2.47	Pathogenic	0.76	Tolerated	4.32	4	0	1	2.2	14.03
c.2668C>T	R890C		Benign		1	6-33443220-C-T	9	5.58e-6	-5.786	Likely Benign	0.402	Ambiguous	Likely Benign	0.200	Likely Benign										-3.38	Deleterious	1.000	Probably Damaging	0.971	Probably Damaging	3.94	Benign	0.04	Affected	4.32	4	-4	-3	7.0	-53.05
c.2669G>A	R890H		Uncertain		1	6-33443221-G-A	19	1.18e-5	-3.600	Likely Benign	0.198	Likely Benign	Likely Benign	0.056	Likely Benign										-1.29	Neutral	0.254	Benign	0.134	Benign	3.97	Benign	0.15	Tolerated	4.32	4	2	0	1.3	-19.05
c.2669G>C	R890P		Likely Benign		2	6-33443221-G-C	28	1.74e-5	-1.931	Likely Benign	0.301	Likely Benign	Likely Benign	0.191	Likely Benign										-1.21	Neutral	0.999	Probably Damaging	0.977	Probably Damaging	4.02	Benign	0.28	Tolerated	4.32	4	0	-2	2.9	-59.07
c.266C>T	P89L		Uncertain		2				-6.775	Likely Benign	0.982	Likely Pathogenic	Likely Pathogenic	0.119	Likely Benign										-3.29	Deleterious	0.889	Possibly Damaging	0.058	Benign	3.73	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.2674T>C	S892P					6-33443226-T-C	1	6.20e-7	-3.247	Likely Benign	0.222	Likely Benign	Likely Benign	0.041	Likely Benign										-0.87	Neutral	0.057	Benign	0.047	Benign	2.60	Benign	0.01	Affected	4.32	4	-1	1	-0.8	10.04
c.2678A>C	Q893P					6-33443230-A-C	1	6.20e-7	-2.463	Likely Benign	0.072	Likely Benign	Likely Benign	0.084	Likely Benign										-0.70	Neutral	0.802	Possibly Damaging	0.432	Benign	2.69	Benign	0.05	Affected	4.32	4	-1	0	1.9	-31.01
c.2681G>A	G894E		Uncertain		1	6-33443233-G-A	6	3.72e-6	-5.377	Likely Benign	0.859	Likely Pathogenic	Ambiguous	0.180	Likely Benign										-2.07	Neutral	1.000	Probably Damaging	1.000	Probably Damaging	2.68	Benign	0.01	Affected	4.32	4	0	-2	-3.1	72.06
c.2681G>C	G894A					6-33443233-G-C	1	6.20e-7	-3.997	Likely Benign	0.267	Likely Benign	Likely Benign	0.180	Likely Benign										-1.26	Neutral	0.999	Probably Damaging	0.999	Probably Damaging	2.69	Benign	0.97	Tolerated	4.32	4	0	1	2.2	14.03
c.2683A>C	S895R					6-33443235-A-C	1	6.20e-7	-4.746	Likely Benign	0.973	Likely Pathogenic	Likely Pathogenic	0.167	Likely Benign										-1.72	Neutral	0.997	Probably Damaging	0.995	Probably Damaging	2.64	Benign	0.10	Tolerated	4.32	4	-1	0	-3.7	69.11
c.2684G>A	S895N		Uncertain		1				-6.399	Likely Benign	0.604	Likely Pathogenic	Likely Benign	0.118	Likely Benign										-0.85	Neutral	0.991	Probably Damaging	0.988	Probably Damaging	2.64	Benign	0.30	Tolerated	4.32	4	1	1	-2.7	27.03
c.2684G>C	S895T					6-33443236-G-C	1	6.20e-7	-5.515	Likely Benign	0.199	Likely Benign	Likely Benign	0.132	Likely Benign										-1.14	Neutral	0.979	Probably Damaging	0.982	Probably Damaging	2.75	Benign	0.26	Tolerated	4.32	4	1	1	0.1	14.03
c.2687G>T	G896V					6-33443239-G-T	1	6.20e-7	-2.936	Likely Benign	0.285	Likely Benign	Likely Benign	0.165	Likely Benign										-1.96	Neutral	0.997	Probably Damaging	0.912	Probably Damaging	2.46	Pathogenic	0.30	Tolerated	4.32	4	-3	-1	4.6	42.08
c.268G>A	V90M					6-33425876-G-A	1	6.20e-7	-5.017	Likely Benign	0.463	Ambiguous	Likely Benign	0.053	Likely Benign										-0.15	Neutral	0.872	Possibly Damaging	0.162	Benign	3.98	Benign	0.00	Affected	4.32	1	1	2	-2.3	32.06
c.2690C>T	S897L		Uncertain		1				-4.034	Likely Benign	0.299	Likely Benign	Likely Benign	0.028	Likely Benign										-1.71	Neutral	0.901	Possibly Damaging	0.636	Possibly Damaging	2.66	Benign	0.01	Affected			-3	-2	4.6	26.08
c.2693C>G	S898C					6-33443245-C-G	1	6.20e-7	-7.007	In-Between	0.257	Likely Benign	Likely Benign	0.146	Likely Benign										-2.43	Neutral	0.999	Probably Damaging	0.986	Probably Damaging	2.43	Pathogenic	0.01	Affected	4.32	4	-1	0	3.3	16.06
c.2695A>G	I899V		Uncertain		1	6-33443247-A-G	6	3.72e-6	-2.569	Likely Benign	0.074	Likely Benign	Likely Benign	0.040	Likely Benign										0.09	Neutral	0.220	Benign	0.078	Benign	2.75	Benign	0.92	Tolerated	4.32	4	4	3	-0.3	-14.03
c.2696T>C	I899T					6-33443248-T-C	2	1.24e-6	-2.472	Likely Benign	0.521	Ambiguous	Likely Benign	0.103	Likely Benign										-0.25	Neutral	0.245	Benign	0.096	Benign	2.75	Benign	0.01	Affected	4.32	4	-1	0	-5.2	-12.05
c.2699C>T	T900M		Conflicting		2	6-33443251-C-T	14	8.68e-6	-3.852	Likely Benign	0.176	Likely Benign	Likely Benign	0.015	Likely Benign										-0.81	Neutral	0.060	Benign	0.016	Benign	2.79	Benign	0.08	Tolerated	4.32	4	-1	-1	2.6	30.09
c.269T>A	V90E		Uncertain		1				-4.079	Likely Benign	0.703	Likely Pathogenic	Likely Benign	0.108	Likely Benign										-0.38	Neutral	0.001	Benign	0.000	Benign	4.00	Benign	0.00	Affected	4.32	1	-2	-2	-7.7	29.98
c.26A>G	H9R					6-33420290-A-G			-1.736	Likely Benign	0.112	Likely Benign	Likely Benign	0.113	Likely Benign										-0.04	Neutral	0.012	Benign	0.002	Benign	4.25	Benign	0.00	Affected	4.32	1	0	2	-1.3	19.05
c.2702C>T	A901V		Uncertain		2	6-33443254-C-T	2	1.24e-6	-5.043	Likely Benign	0.219	Likely Benign	Likely Benign	0.029	Likely Benign										-1.83	Neutral	0.106	Benign	0.009	Benign	2.64	Benign	0.17	Tolerated	3.77	5	0	0	2.4	28.05
c.2704G>A	A902T		Likely Benign		1	6-33443256-G-A	36	2.23e-5	-4.966	Likely Benign	0.116	Likely Benign	Likely Benign	0.075	Likely Benign										-1.11	Neutral	0.951	Possibly Damaging	0.617	Possibly Damaging	2.61	Benign	0.01	Affected	3.77	5	1	0	-2.5	30.03
c.2707G>A	G903S					6-33443259-G-A	1	6.20e-7	-3.451	Likely Benign	0.154	Likely Benign	Likely Benign	0.091	Likely Benign										-1.37	Neutral	0.989	Probably Damaging	0.871	Possibly Damaging	2.40	Pathogenic	0.04	Affected	3.77	5	0	1	-0.4	30.03
c.2710A>G	M904V		Likely Benign		2	6-33443262-A-G	77	4.78e-5	-2.907	Likely Benign	0.112	Likely Benign	Likely Benign	0.058	Likely Benign										-0.33	Neutral	0.039	Benign	0.023	Benign	2.80	Benign	0.10	Tolerated	3.77	5	2	1	2.3	-32.06
c.2711T>C	M904T		Uncertain		1				-2.721	Likely Benign	0.668	Likely Pathogenic	Likely Benign	0.042	Likely Benign										-1.15	Neutral	0.277	Benign	0.103	Benign	2.78	Benign	0.18	Tolerated	3.77	5	-1	-1	-2.6	-30.09
c.2713C>A	R905S					6-33443265-C-A	1	6.20e-7	-2.382	Likely Benign	0.903	Likely Pathogenic	Ambiguous	0.133	Likely Benign										-1.39	Neutral	0.999	Probably Damaging	0.962	Probably Damaging	2.71	Benign	0.15	Tolerated	3.77	5	-1	0	3.7	-69.11
c.2713C>T	R905C		Conflicting		2	6-33443265-C-T	15	9.31e-6	-5.578	Likely Benign	0.723	Likely Pathogenic	Likely Benign	0.194	Likely Benign										-3.14	Deleterious	1.000	Probably Damaging	0.980	Probably Damaging	2.57	Benign	0.01	Affected	3.77	5	-4	-3	7.0	-53.05
c.2714G>A	R905H		Uncertain		1	6-33443266-G-A	8	4.96e-6	-4.182	Likely Benign	0.457	Ambiguous	Likely Benign	0.192	Likely Benign										-1.11	Neutral	1.000	Probably Damaging	0.991	Probably Damaging	2.59	Benign	0.09	Tolerated	3.77	5	2	0	1.3	-19.05
c.2714G>T	R905L					6-33443266-G-T			-3.284	Likely Benign	0.709	Likely Pathogenic	Likely Benign	0.242	Likely Benign										-2.55	Deleterious	0.963	Probably Damaging	0.753	Possibly Damaging	2.61	Benign	0.10	Tolerated	3.77	5	-2	-3	8.3	-43.03
c.2719A>T	S907C		Uncertain		1				-6.685	Likely Benign	0.298	Likely Benign	Likely Benign	0.113	Likely Benign										-2.34	Neutral	0.999	Probably Damaging	0.988	Probably Damaging	2.60	Benign	0.02	Affected	3.77	5	0	-1	3.3	16.06
c.2724G>C	Q908H		Conflicting		4	6-33443276-G-C	1	6.20e-7	-4.658	Likely Benign	0.310	Likely Benign	Likely Benign	0.112	Likely Benign										-0.74	Neutral	0.996	Probably Damaging	0.995	Probably Damaging	2.58	Benign	0.05	Affected	3.77	5	3	0	0.3	9.01
c.2725A>T	M909L					6-33443277-A-T	4	2.48e-6	-1.417	Likely Benign	0.152	Likely Benign	Likely Benign	0.184	Likely Benign										-0.85	Neutral	0.002	Benign	0.006	Benign	2.82	Benign	0.32	Tolerated	3.77	5	2	4	1.9	-18.03
c.2729G>C	G910A		Uncertain		1	6-33443281-G-C	1	6.20e-7	-3.587	Likely Benign	0.360	Ambiguous	Likely Benign	0.209	Likely Benign										-1.43	Neutral	0.999	Probably Damaging	0.999	Probably Damaging	2.78	Benign	0.10	Tolerated	3.77	5	1	0	2.2	14.03
c.2729G>T	G910V					6-33443281-G-T	1	6.20e-7	-4.362	Likely Benign	0.724	Likely Pathogenic	Likely Benign	0.237	Likely Benign										-2.69	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.73	Benign	0.02	Affected	3.77	5	-3	-1	4.6	42.08
c.272A>G	E91G		Likely Benign		1				-3.226	Likely Benign	0.783	Likely Pathogenic	Likely Benign	0.110	Likely Benign										-2.18	Neutral	0.947	Possibly Damaging	0.727	Possibly Damaging	3.86	Benign	0.00	Affected	4.32	1	0	-2	3.1	-72.06
c.2735C>A	T912N		Uncertain		1				-4.260	Likely Benign	0.190	Likely Benign	Likely Benign	0.116	Likely Benign										-1.15	Neutral	0.999	Probably Damaging	0.977	Probably Damaging	3.96	Benign	0.00	Affected	3.77	5	0	0	-2.8	13.00
c.2735C>T	T912I					6-33443287-C-T	2	1.24e-6	-4.461	Likely Benign	0.522	Ambiguous	Likely Benign	0.117	Likely Benign										-1.27	Neutral	0.999	Probably Damaging	0.977	Probably Damaging	3.95	Benign	0.00	Affected	3.77	5	-1	0	5.2	12.05
c.273G>C	E91D					6-33425881-G-C	1	6.20e-7	-3.160	Likely Benign	0.293	Likely Benign	Likely Benign	0.095	Likely Benign										-0.84	Neutral	0.880	Possibly Damaging	0.636	Possibly Damaging	3.98	Benign	0.00	Affected	4.32	1	2	3	0.0	-14.03
c.2741A>T	D914V		Uncertain		1				-4.260	Likely Benign	0.723	Likely Pathogenic	Likely Benign	0.187	Likely Benign										-2.24	Neutral	0.999	Probably Damaging	0.986	Probably Damaging	2.64	Benign	0.01	Affected	3.77	5	-3	-2	7.7	-15.96
c.2742C>A	D914E					6-33443294-C-A	5	3.10e-6	-3.231	Likely Benign	0.170	Likely Benign	Likely Benign	0.133	Likely Benign										-0.29	Neutral	0.893	Possibly Damaging	0.418	Benign	2.87	Benign	1.00	Tolerated	3.77	5	2	3	0.0	14.03
c.2743G>A	G915S		Uncertain		1	6-33443295-G-A	9	5.58e-6	-3.557	Likely Benign	0.083	Likely Benign	Likely Benign	0.050	Likely Benign										-0.88	Neutral	0.801	Possibly Damaging	0.201	Benign	2.73	Benign	0.31	Tolerated	3.77	5	1	0	-0.4	30.03
c.2743G>T	G915C					6-33443295-G-T	1	6.20e-7	-6.446	Likely Benign	0.185	Likely Benign	Likely Benign	0.103	Likely Benign										-2.84	Deleterious	1.000	Probably Damaging	0.989	Probably Damaging	2.64	Benign	0.01	Affected	3.77	5	-3	-3	2.9	46.09
c.2744G>T	G915V					6-33443296-G-T			-4.586	Likely Benign	0.189	Likely Benign	Likely Benign	0.149	Likely Benign										-2.52	Deleterious	0.997	Probably Damaging	0.918	Probably Damaging	2.68	Benign	0.01	Affected	3.77	5	-3	-1	4.6	42.08
c.2746G>A	V916I					6-33443298-G-A	25	1.55e-5	-4.336	Likely Benign	0.074	Likely Benign	Likely Benign	0.062	Likely Benign										-0.05	Neutral	0.010	Benign	0.015	Benign	2.71	Benign	0.09	Tolerated	3.77	5	3	4	0.3	14.03
c.2749C>G	P917A					6-33443301-C-G	1	6.20e-7	-3.681	Likely Benign	0.062	Likely Benign	Likely Benign	0.053	Likely Benign										-1.33	Neutral	0.065	Benign	0.037	Benign	2.72	Benign	0.00	Affected	3.77	5	-1	1	3.4	-26.04
c.2749C>T	P917S					6-33443301-C-T	1	6.20e-7	-3.562	Likely Benign	0.072	Likely Benign	Likely Benign	0.056	Likely Benign										-0.54	Neutral	0.003	Benign	0.002	Benign	2.70	Benign	0.00	Affected	3.77	5	-1	1	0.8	-10.04
c.274G>A	G92R					6-33425882-G-A	1	6.20e-7	-2.909	Likely Benign	0.876	Likely Pathogenic	Ambiguous	0.139	Likely Benign										-2.38	Neutral	0.999	Probably Damaging	0.979	Probably Damaging	4.01	Benign	0.00	Affected	4.32	1	-2	-3	-4.1	99.14
c.2750C>G	P917R					6-33443302-C-G	5	3.10e-6	-4.475	Likely Benign	0.363	Ambiguous	Likely Benign	0.142	Likely Benign										-1.70	Neutral	0.642	Possibly Damaging	0.316	Benign	2.68	Benign	0.00	Affected	3.77	5	-2	0	-2.9	59.07
c.2752G>A	A918T					6-33443304-G-A	1	6.20e-7	-4.139	Likely Benign	0.083	Likely Benign	Likely Benign	0.065	Likely Benign										-1.09	Neutral	0.980	Probably Damaging	0.721	Possibly Damaging	2.64	Benign	0.03	Affected	4.32	4	0	1	-2.5	30.03
c.2753C>T	A918V		Uncertain		3	6-33443305-C-T	2	1.24e-6	-3.684	Likely Benign	0.112	Likely Benign	Likely Benign	0.119	Likely Benign										-1.61	Neutral	0.980	Probably Damaging	0.782	Possibly Damaging	2.61	Benign	0.03	Affected	4.32	4	0	0	2.4	28.05
c.2756A>T	Q919L					6-33443308-A-T	1	6.20e-7	-4.492	Likely Benign	0.252	Likely Benign	Likely Benign	0.175	Likely Benign										-2.13	Neutral	0.891	Possibly Damaging	0.596	Possibly Damaging	2.40	Pathogenic	0.04	Affected	4.32	4	-2	-2	7.3	-14.97
c.2762T>C	L921P					6-33443314-T-C	1	6.20e-7	-2.087	Likely Benign	0.393	Ambiguous	Likely Benign	0.215	Likely Benign										-1.83	Neutral	0.998	Probably Damaging	0.958	Probably Damaging	2.39	Pathogenic	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.2765G>A	R922Q		Uncertain		1	6-33443317-G-A	7	4.34e-6	-3.295	Likely Benign	0.189	Likely Benign	Likely Benign	0.085	Likely Benign										-0.27	Neutral	0.992	Probably Damaging	0.736	Possibly Damaging	2.57	Benign	0.20	Tolerated	3.77	5	1	1	1.0	-28.06
c.2767A>G	I923V					6-33443319-A-G	1	6.20e-7	-2.010	Likely Benign	0.113	Likely Benign	Likely Benign	0.059	Likely Benign										0.05	Neutral	0.028	Benign	0.009	Benign	2.76	Benign	1.00	Tolerated	3.77	5	3	4	-0.3	-14.03
c.2768T>A	I923N		Uncertain		1				-0.733	Likely Benign	0.712	Likely Pathogenic	Likely Benign	0.108	Likely Benign										-1.16	Neutral	0.991	Probably Damaging	0.793	Possibly Damaging	2.70	Benign	0.13	Tolerated	3.77	5	-2	-3	-8.0	0.94
c.277C>G	R93G		Uncertain		1				-2.674	Likely Benign	0.400	Ambiguous	Likely Benign	0.093	Likely Benign										-1.69	Neutral	0.103	Benign	0.019	Benign	3.99	Benign	0.00	Affected	4.32	1	-2	-3	4.1	-99.14
c.2783A>G	Q928R					6-33443335-A-G	1	6.20e-7	-4.089	Likely Benign	0.826	Likely Pathogenic	Ambiguous	0.290	Likely Benign										-2.91	Deleterious	0.994	Probably Damaging	0.988	Probably Damaging	1.58	Pathogenic	0.00	Affected	4.32	4	1	1	-1.0	28.06
c.2800A>G	M934V					6-33443352-A-G	1	6.20e-7	-3.286	Likely Benign	0.218	Likely Benign	Likely Benign	0.119	Likely Benign										-2.06	Neutral	0.166	Benign	0.101	Benign	2.47	Pathogenic	0.39	Tolerated	3.77	5	1	2	2.3	-32.06
c.2806G>A	A936T					6-33443358-G-A	1	6.20e-7	-4.540	Likely Benign	0.091	Likely Benign	Likely Benign	0.047	Likely Benign										-0.50	Neutral	0.051	Benign	0.033	Benign	2.67	Benign	0.09	Tolerated	3.77	5	0	1	-2.5	30.03
c.2807C>T	A936V					6-33443359-C-T	4	2.48e-6	-4.787	Likely Benign	0.226	Likely Benign	Likely Benign	0.089	Likely Benign										-1.58	Neutral	0.801	Possibly Damaging	0.192	Benign	2.48	Pathogenic	0.19	Tolerated	3.77	5	0	0	2.4	28.05
c.2809G>C	D937H		Uncertain		1				-0.733	Likely Benign	0.677	Likely Pathogenic	Likely Benign	0.150	Likely Benign										-1.74	Neutral	1.000	Probably Damaging	0.975	Probably Damaging	2.68	Benign	0.13	Tolerated	3.77	5	-1	1	0.3	22.05
c.280C>A	P94T					6-33425888-C-A	1	6.20e-7	-4.254	Likely Benign	0.085	Likely Benign	Likely Benign	0.088	Likely Benign										-2.35	Neutral	0.198	Benign	0.015	Benign	4.12	Benign	0.00	Affected	4.32	1	-1	0	0.9	3.99
c.280C>T	P94S		Uncertain		1	6-33425888-C-T	5	3.10e-6	-3.151	Likely Benign	0.084	Likely Benign	Likely Benign	0.093	Likely Benign										-2.36	Neutral	0.092	Benign	0.008	Benign	4.13	Benign	0.00	Affected	4.32	1	1	-1	0.8	-10.04
c.2812G>A	G938R		Uncertain		1				-5.271	Likely Benign	0.732	Likely Pathogenic	Likely Benign	0.141	Likely Benign										-1.11	Neutral	0.999	Probably Damaging	0.985	Probably Damaging	2.74	Benign	0.36	Tolerated	3.77	5	-3	-2	-4.1	99.14
c.2816C>G	P939R					6-33443368-C-G	1	6.20e-7	-4.863	Likely Benign	0.260	Likely Benign	Likely Benign	0.199	Likely Benign										-3.79	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.18	Pathogenic	0.00	Affected	3.77	5	-2	0	-2.9	59.07
c.2818G>A	G940S		Uncertain		1	6-33443370-G-A	1	6.20e-7	-5.451	Likely Benign	0.084	Likely Benign	Likely Benign	0.135	Likely Benign										0.45	Neutral	0.409	Benign	0.253	Benign	2.77	Benign	0.44	Tolerated	3.77	5	1	0	-0.4	30.03
c.2818G>C	G940R		Benign		1	6-33443370-G-C	5	3.10e-6	-6.169	Likely Benign	0.480	Ambiguous	Likely Benign	0.060	Likely Benign										0.02	Neutral	0.922	Possibly Damaging	0.543	Possibly Damaging	2.73	Benign	0.15	Tolerated	3.77	5	-3	-2	-4.1	99.14
c.2819G>A	G940D					6-33443371-G-A	6	3.72e-6	-7.311	In-Between	0.397	Ambiguous	Likely Benign	0.076	Likely Benign										-0.68	Neutral	0.770	Possibly Damaging	0.583	Possibly Damaging	2.72	Benign	0.17	Tolerated	3.77	5	-1	1	-3.1	58.04
c.281C>A	P94H					6-33425889-C-A	1	6.20e-7	-3.708	Likely Benign	0.106	Likely Benign	Likely Benign	0.077	Likely Benign										-2.31	Neutral	0.637	Possibly Damaging	0.102	Benign	4.11	Benign	0.00	Affected	4.32	1	-2	0	-1.6	40.02
c.2821C>A	P941T					6-33443373-C-A	2	1.24e-6	-6.193	Likely Benign	0.065	Likely Benign	Likely Benign	0.033	Likely Benign										0.19	Neutral	0.144	Benign	0.085	Benign	2.77	Benign	0.05	Affected	4.32	4	-1	0	0.9	3.99
c.2821C>G	P941A					6-33443373-C-G	2	1.24e-6	-4.313	Likely Benign	0.054	Likely Benign	Likely Benign	0.046	Likely Benign										0.10	Neutral	0.000	Benign	0.002	Benign	2.80	Benign	0.10	Tolerated	4.32	4	-1	1	3.4	-26.04
c.2821C>T	P941S					6-33443373-C-T	1	6.20e-7	-5.099	Likely Benign	0.062	Likely Benign	Likely Benign	0.039	Likely Benign										0.58	Neutral	0.036	Benign	0.039	Benign	3.05	Benign	0.95	Tolerated	4.32	4	-1	1	0.8	-10.04
c.2822C>T	P941L		Uncertain		1				-5.692	Likely Benign	0.066	Likely Benign	Likely Benign	0.054	Likely Benign										-0.44	Neutral	0.144	Benign	0.039	Benign	2.76	Benign	0.01	Affected			-3	-3	5.4	16.04
c.2824C>T	P942S					6-33443376-C-T	1	6.20e-7	-3.919	Likely Benign	0.062	Likely Benign	Likely Benign	0.036	Likely Benign										-0.80	Neutral	0.011	Benign	0.015	Benign	2.43	Pathogenic	0.00	Affected	4.32	4	-1	1	0.8	-10.04
c.2825C>T	P942L		Uncertain		1	6-33443377-C-T	4	2.48e-6	-5.063	Likely Benign	0.086	Likely Benign	Likely Benign	0.048	Likely Benign										-2.00	Neutral	0.411	Benign	0.239	Benign	2.37	Pathogenic	0.00	Affected	4.32	4	-3	-3	5.4	16.04
c.2827G>C	G943R					6-33443379-G-C	1	6.20e-7	-7.159	In-Between	0.335	Likely Benign	Likely Benign	0.308	Likely Benign										1.00	Neutral	0.411	Benign	0.062	Benign	2.86	Benign	0.94	Tolerated	4.32	4	-2	-3	-4.1	99.14
c.2828G>C	G943A					6-33443380-G-C	3	1.86e-6	-6.684	Likely Benign	0.070	Likely Benign	Likely Benign	0.274	Likely Benign										0.10	Neutral	0.001	Benign	0.002	Benign	2.87	Benign	0.89	Tolerated	4.32	4	0	1	2.2	14.03
c.2830G>A	G944S		Benign		1	6-33443382-G-A	13	8.05e-6	-5.303	Likely Benign	0.082	Likely Benign	Likely Benign	0.223	Likely Benign										-0.75	Neutral	0.007	Benign	0.004	Benign	3.77	Benign	0.00	Affected	4.32	4	1	0	-0.4	30.03
c.2830G>T	G944C					6-33443382-G-T	1	6.20e-7	-9.121	Likely Pathogenic	0.093	Likely Benign	Likely Benign	0.426	Likely Benign										-1.79	Neutral	0.975	Probably Damaging	0.848	Possibly Damaging	3.70	Benign	0.00	Affected	4.32	4	-3	-3	2.9	46.09
c.2831G>T	G944V					6-33443383-G-T	1	6.20e-7	-7.536	In-Between	0.089	Likely Benign	Likely Benign	0.446	Likely Benign										-1.41	Neutral	0.126	Benign	0.096	Benign	3.70	Benign	0.00	Affected	4.32	4	-3	-1	4.6	42.08
c.2834A>G	H945R					6-33443386-A-G	1	6.20e-7	-5.186	Likely Benign	0.118	Likely Benign	Likely Benign	0.333	Likely Benign										-0.59	Neutral	0.982	Probably Damaging	0.903	Possibly Damaging	5.05	Benign	0.08	Tolerated	4.32	4	0	2	-1.3	19.05
c.2834A>T	H945L					6-33443386-A-T	2	1.24e-6	-4.741	Likely Benign	0.088	Likely Benign	Likely Benign	0.399	Likely Benign										0.16	Neutral	0.948	Possibly Damaging	0.863	Possibly Damaging	5.05	Benign	1.00	Tolerated	4.32	4	-3	-2	7.0	-23.98
c.2835T>A	H945Q		Conflicting		2	6-33443387-T-A	3	1.86e-6	-5.248	Likely Benign	0.091	Likely Benign	Likely Benign	0.343	Likely Benign										-0.36	Neutral	0.995	Probably Damaging	0.939	Probably Damaging	5.03	Benign	0.06	Tolerated	4.32	4	3	0	-0.3	-9.01
c.2837G>A	G946E		Benign		3	6-33443389-G-A	13	8.05e-6	-8.793	Likely Pathogenic	0.257	Likely Benign	Likely Benign	0.341	Likely Benign										-0.51	Neutral	0.818	Possibly Damaging	0.355	Benign	4.58	Benign	0.00	Affected	4.32	4	0	-2	-3.1	72.06
c.2839G>A	G947R					6-33443391-G-A	6	3.72e-6	-7.481	In-Between	0.343	Ambiguous	Likely Benign	0.273	Likely Benign										-0.60	Neutral	0.411	Benign	0.140	Benign	4.94	Benign	0.04	Affected	4.32	4	-2	-3	-4.1	99.14
c.283C>G	H95D					6-33425891-C-G	3	1.86e-6	-2.387	Likely Benign	0.188	Likely Benign	Likely Benign	0.092	Likely Benign										-0.81	Neutral	0.084	Benign	0.009	Benign	4.22	Benign	0.00	Affected	4.32	1	-1	1	-0.3	-22.05
c.2840G>A	G947E					6-33443392-G-A	1	6.20e-7	-9.574	Likely Pathogenic	0.243	Likely Benign	Likely Benign	0.302	Likely Benign										0.08	Neutral	0.126	Benign	0.096	Benign	4.92	Benign	0.10	Tolerated	4.32	4	-2	0	-3.1	72.06
c.2840G>C	G947A		Likely Benign		1	6-33443392-G-C	28	1.73e-5	-6.511	Likely Benign	0.080	Likely Benign	Likely Benign	0.156	Likely Benign										-0.41	Neutral	0.224	Benign	0.131	Benign	4.97	Benign	0.10	Tolerated	4.32	4	1	0	2.2	14.03
c.2845G>A	G949S		Benign/Likely benign		4	6-33443397-G-A	122	7.56e-5	-5.693	Likely Benign	0.072	Likely Benign	Likely Benign	0.321	Likely Benign										0.30	Neutral	0.611	Possibly Damaging	0.102	Benign	2.23	Pathogenic	0.00	Affected	4.32	4	1	0	-0.4	30.03																10.1016/j.ajhg.2020.11.011
c.284A>G	H95R					6-33425892-A-G	1	6.20e-7	-2.789	Likely Benign	0.153	Likely Benign	Likely Benign	0.043	Likely Benign										-1.31	Neutral	0.084	Benign	0.009	Benign	4.20	Benign	0.00	Affected	4.32	1	0	2	-1.3	19.05
c.2852A>G	H951R		Likely Pathogenic		1				-4.964	Likely Benign	0.125	Likely Benign	Likely Benign	0.185	Likely Benign										-1.08	Neutral	0.048	Benign	0.029	Benign	5.46	Benign	0.24	Tolerated	3.77	5	2	0	-1.3	19.05
c.2854G>A	G952S		Conflicting		2	6-33443406-G-A	2	1.24e-6	-6.190	Likely Benign	0.076	Likely Benign	Likely Benign	0.167	Likely Benign										0.19	Neutral	0.000	Benign	0.002	Benign	3.31	Benign	0.07	Tolerated	3.77	5	1	0	-0.4	30.03
c.2855G>T	G952V		Uncertain		1				-7.074	In-Between	0.078	Likely Benign	Likely Benign	0.231	Likely Benign										-0.33	Neutral	0.000	Benign	0.000	Benign	3.20	Benign	0.02	Affected	3.77	5	-1	-3	4.6	42.08
c.2858C>A	P953Q		Uncertain		1				-6.038	Likely Benign	0.079	Likely Benign	Likely Benign	0.086	Likely Benign										-0.78	Neutral	0.058	Benign	0.015	Benign	2.78	Benign	0.29	Tolerated	3.77	5	0	-1	-1.9	31.01
c.2858C>T	P953L					6-33443410-C-T	11	6.82e-6	-6.069	Likely Benign	0.079	Likely Benign	Likely Benign	0.087	Likely Benign										-1.34	Neutral	0.611	Possibly Damaging	0.096	Benign	2.76	Benign	0.25	Tolerated	3.77	5	-3	-3	5.4	16.04
c.285C>A	H95Q					6-33425893-C-A	1	6.20e-7	-3.355	Likely Benign	0.084	Likely Benign	Likely Benign	0.070	Likely Benign										-0.97	Neutral	0.633	Possibly Damaging	0.017	Benign	4.21	Benign	0.00	Affected	4.32	1	0	3	-0.3	-9.01
c.2860C>T	P954S		Likely Benign		1	6-33443412-C-T	1	6.20e-7	-3.525	Likely Benign	0.062	Likely Benign	Likely Benign	0.143	Likely Benign										-0.25	Neutral	0.954	Possibly Damaging	0.812	Possibly Damaging	2.87	Benign	1.00	Tolerated	3.77	5	1	-1	0.8	-10.04
c.2863T>C	S955P		Uncertain		1	6-33443415-T-C	3	1.86e-6	-2.584	Likely Benign	0.073	Likely Benign	Likely Benign	0.098	Likely Benign										-0.75	Neutral	0.001	Benign	0.004	Benign	2.33	Pathogenic	0.00	Affected	3.77	5	1	-1	-0.8	10.04
c.2864C>T	S955F		Conflicting		4	6-33443416-C-T	95	5.89e-5	-7.374	In-Between	0.176	Likely Benign	Likely Benign	0.093	Likely Benign										-1.73	Neutral	0.977	Probably Damaging	0.721	Possibly Damaging	2.32	Pathogenic	0.00	Affected	3.77	5	-3	-2	3.6	60.10
c.2869C>T	H957Y					6-33443421-C-T	1	6.20e-7	-6.631	Likely Benign	0.129	Likely Benign	Likely Benign	0.099	Likely Benign										-1.00	Neutral	0.510	Possibly Damaging	0.147	Benign	2.42	Pathogenic	0.10	Tolerated	3.77	5	2	0	1.9	26.03
c.286G>A	G96S		Uncertain		1	6-33425894-G-A	5	3.10e-6	-3.049	Likely Benign	0.065	Likely Benign	Likely Benign	0.071	Likely Benign										-0.76	Neutral	0.364	Benign	0.008	Benign	4.25	Benign	0.00	Affected	4.32	1	1	0	-0.4	30.03
c.2870A>G	H957R					6-33443422-A-G	1	6.20e-7	-6.723	Likely Benign	0.183	Likely Benign	Likely Benign	0.105	Likely Benign										-1.31	Neutral	0.144	Benign	0.078	Benign	2.58	Benign	0.32	Tolerated	3.77	5	0	2	-1.3	19.05
c.2873A>C	H958P		Benign		1	6-33443425-A-C	2	1.24e-6	-8.369	Likely Pathogenic	0.068	Likely Benign	Likely Benign	0.204	Likely Benign										-0.36	Neutral	0.925	Possibly Damaging	0.316	Benign	4.14	Benign	0.10	Tolerated	3.77	5	0	-2	1.6	-40.02
c.2875C>G	H959D					6-33443427-C-G	1	6.20e-7	-12.060	Likely Pathogenic	0.235	Likely Benign	Likely Benign	0.176	Likely Benign										-0.73	Neutral	0.144	Benign	0.058	Benign	4.14	Benign	0.29	Tolerated	3.77	5	-1	1	-0.3	-22.05
c.2878C>T	H960Y					6-33443430-C-T	1	6.20e-7	-8.181	Likely Pathogenic	0.158	Likely Benign	Likely Benign	0.097	Likely Benign										-1.25	Neutral	0.748	Possibly Damaging	0.232	Benign	4.13	Benign	0.21	Tolerated	3.77	5	2	0	1.9	26.03
c.2879A>G	H960R					6-33443431-A-G	1	6.20e-7	-9.238	Likely Pathogenic	0.192	Likely Benign	Likely Benign	0.075	Likely Benign										-1.10	Neutral	0.494	Possibly Damaging	0.170	Benign	4.19	Benign	0.25	Tolerated	3.77	5	0	2	-1.3	19.05
c.2881C>T	H961Y		Conflicting		2	6-33443433-C-T	3	1.86e-6	-8.051	Likely Pathogenic	0.157	Likely Benign	Likely Benign	0.102	Likely Benign										-1.07	Neutral	0.716	Possibly Damaging	0.147	Benign	4.10	Benign	0.55	Tolerated	3.77	5	0	2	1.9	26.03
c.2887C>T	H963Y					6-33443439-C-T	1	6.20e-7	-7.557	In-Between	0.158	Likely Benign	Likely Benign	0.105	Likely Benign										-1.13	Neutral	0.812	Possibly Damaging	0.298	Benign	4.09	Benign	0.10	Tolerated	3.77	5	2	0	1.9	26.03
c.2888A>G	H963R		Uncertain		1	6-33443440-A-G	8	4.96e-6	-8.952	Likely Pathogenic	0.169	Likely Benign	Likely Benign	0.081	Likely Benign										-1.28	Neutral	0.001	Benign	0.003	Benign	4.15	Benign	0.24	Tolerated	3.77	5	2	0	-1.3	19.05
c.2893C>G	H965D					6-33443445-C-G	1	6.20e-7	-9.827	Likely Pathogenic	0.192	Likely Benign	Likely Benign	0.147	Likely Benign										-0.94	Neutral	0.007	Benign	0.018	Benign	4.09	Benign	0.62	Tolerated	3.77	5	-1	1	-0.3	-22.05
c.2894A>G	H965R					6-33443446-A-G	1	6.20e-7	-7.056	In-Between	0.156	Likely Benign	Likely Benign	0.104	Likely Benign										-0.88	Neutral	0.065	Benign	0.049	Benign	4.08	Benign	0.38	Tolerated	3.77	5	0	2	-1.3	19.05
c.2896C>G	H966D					6-33443448-C-G	1	6.20e-7	-8.426	Likely Pathogenic	0.201	Likely Benign	Likely Benign	0.182	Likely Benign										-1.09	Neutral	0.494	Possibly Damaging	0.170	Benign	4.05	Benign	0.93	Tolerated	4.32	2	-1	1	-0.3	-22.05
c.2896C>T	H966Y					6-33443448-C-T			-6.847	Likely Benign	0.126	Likely Benign	Likely Benign	0.106	Likely Benign										-1.27	Neutral	0.878	Possibly Damaging	0.232	Benign	4.01	Benign	0.23	Tolerated	4.32	2	2	0	1.9	26.03
c.2897A>G	H966R					6-33443449-A-G			-5.474	Likely Benign	0.157	Likely Benign	Likely Benign	0.172	Likely Benign										-0.71	Neutral	0.494	Possibly Damaging	0.170	Benign	4.06	Benign	0.69	Tolerated	4.32	2	0	2	-1.3	19.05
c.2899C>G	R967G					6-33443451-C-G	1	6.20e-7	-2.214	Likely Benign	0.098	Likely Benign	Likely Benign	0.279	Likely Benign										-0.93	Neutral	0.005	Benign	0.007	Benign	4.17	Benign	0.18	Tolerated	4.32	2	-2	-3	4.1	-99.14
c.289G>A	E97K					6-33425897-G-A	1	6.20e-7	-4.972	Likely Benign	0.643	Likely Pathogenic	Likely Benign	0.139	Likely Benign										-0.30	Neutral	0.976	Probably Damaging	0.651	Possibly Damaging	4.16	Benign	0.00	Affected	4.32	1	1	0	-0.4	-0.94
c.289G>C	E97Q					6-33425897-G-C	2	1.24e-6	-3.917	Likely Benign	0.300	Likely Benign	Likely Benign	0.113	Likely Benign										-0.32	Neutral	0.978	Probably Damaging	0.832	Possibly Damaging	4.13	Benign	0.00	Affected	4.32	1	2	2	0.0	-0.98
c.28C>T	R10W		Uncertain		1	6-33420292-C-T	2	1.30e-6	-5.707	Likely Benign	0.503	Ambiguous	Likely Benign	0.236	Likely Benign										-0.31	Neutral	0.964	Probably Damaging	0.190	Benign	4.10	Benign	0.00	Affected	4.32	1	2	-3	3.6	30.03
c.2900G>A	R967Q		Benign/Likely benign		2	6-33443452-G-A	31	1.92e-5	-3.057	Likely Benign	0.080	Likely Benign	Likely Benign	0.104	Likely Benign										-0.01	Neutral	0.994	Probably Damaging	0.626	Possibly Damaging	4.21	Benign	0.36	Tolerated	4.32	2	1	1	1.0	-28.06
c.2900G>T	R967L					6-33443452-G-T	1	6.20e-7	-3.496	Likely Benign	0.164	Likely Benign	Likely Benign	0.123	Likely Benign										-0.99	Neutral	0.959	Probably Damaging	0.586	Possibly Damaging	4.15	Benign	0.75	Tolerated	4.32	2	-2	-3	8.3	-43.03
c.2903G>A	G968D					6-33443455-G-A	1	6.20e-7	-5.134	Likely Benign	0.179	Likely Benign	Likely Benign	0.157	Likely Benign										-0.48	Neutral	0.440	Benign	0.198	Benign	4.19	Benign	0.21	Tolerated	4.32	2	-1	1	-3.1	58.04
c.2908G>C	E970Q					6-33443460-G-C	1	6.20e-7	-2.662	Likely Benign	0.141	Likely Benign	Likely Benign	0.053	Likely Benign										-0.23	Neutral	0.007	Benign	0.006	Benign	4.13	Benign	0.21	Tolerated	4.32	2	2	2	0.0	-0.98
c.2909A>G	E970G		Benign		1				-0.167	Likely Benign	0.139	Likely Benign	Likely Benign	0.139	Likely Benign										-0.93	Neutral	0.144	Benign	0.058	Benign	4.09	Benign	0.10	Tolerated	4.32	2	0	-2	3.1	-72.06
c.290A>T	E97V					6-33425898-A-T	1	6.20e-7	-3.743	Likely Benign	0.514	Ambiguous	Likely Benign	0.124	Likely Benign										-1.17	Neutral	0.947	Possibly Damaging	0.788	Possibly Damaging	4.07	Benign	0.00	Affected	4.32	1	-2	-2	7.7	-29.98
c.2911C>T	P971S					6-33443463-C-T	1	6.20e-7	-4.188	Likely Benign	0.061	Likely Benign	Likely Benign	0.058	Likely Benign										-0.51	Neutral	0.002	Benign	0.003	Benign	3.99	Benign	0.00	Affected	4.32	2	-1	1	0.8	-10.04
c.2912C>A	P971H					6-33443464-C-A	1	6.20e-7	-5.243	Likely Benign	0.086	Likely Benign	Likely Benign	0.039	Likely Benign										-1.11	Neutral	0.898	Possibly Damaging	0.477	Possibly Damaging	3.89	Benign	0.00	Affected	4.32	2	-2	0	-1.6	40.02
c.2914C>G	P972A		Uncertain		1	6-33443466-C-G	1	6.20e-7	-0.167	Likely Benign	0.045	Likely Benign	Likely Benign	0.046	Likely Benign										-0.89	Neutral	0.016	Benign	0.011	Benign	4.29	Benign	0.07	Tolerated	4.32	2	-1	1	3.4	-26.04
c.2914C>T	P972S		Uncertain		1	6-33443466-C-T	4	2.48e-6	-4.008	Likely Benign	0.058	Likely Benign	Likely Benign	0.074	Likely Benign										-0.38	Neutral	0.001	Benign	0.002	Benign	4.28	Benign	0.05	Affected	4.32	2	-1	1	0.8	-10.04
c.2915C>G	P972R					6-33443467-C-G			-4.483	Likely Benign	0.139	Likely Benign	Likely Benign	0.043	Likely Benign										-1.44	Neutral	0.290	Benign	0.114	Benign	4.23	Benign	0.12	Tolerated	4.32	2	-2	0	-2.9	59.07
c.2918G>C	G973A					6-33443470-G-C	1	6.20e-7	-3.847	Likely Benign	0.074	Likely Benign	Likely Benign	0.091	Likely Benign										0.14	Neutral	0.112	Benign	0.028	Benign	4.30	Benign	0.62	Tolerated	4.32	2	0	1	2.2	14.03
c.291G>T	E97D		Uncertain		3	6-33425899-G-T			-3.239	Likely Benign	0.077	Likely Benign	Likely Benign	0.081	Likely Benign										-0.49	Neutral	0.880	Possibly Damaging	0.636	Possibly Damaging	4.12	Benign	0.00	Affected	4.32	1	3	2	0.0	-14.03
c.2924C>A	T975N		Uncertain		1	6-33443476-C-A	1	6.20e-7	-4.671	Likely Benign	0.089	Likely Benign	Likely Benign	0.100	Likely Benign										-0.58	Neutral	0.586	Possibly Damaging	0.302	Benign	4.13	Benign	0.07	Tolerated	4.32	2	0	0	-2.8	13.00
c.2924C>T	T975I		Uncertain		1	6-33443476-C-T	6	3.72e-6	-3.912	Likely Benign	0.164	Likely Benign	Likely Benign	0.068	Likely Benign										-1.66	Neutral	0.411	Benign	0.239	Benign	4.11	Benign	0.66	Tolerated	4.32	2	0	-1	5.2	12.05
c.2928T>A	F976L					6-33443480-T-A	2	1.24e-6	-2.432	Likely Benign	0.825	Likely Pathogenic	Ambiguous	0.212	Likely Benign										-0.87	Neutral	0.264	Benign	0.102	Benign	4.20	Benign	0.53	Tolerated	4.32	2	2	0	1.0	-34.02
c.2928T>G	F976L		Uncertain		1				-2.432	Likely Benign	0.825	Likely Pathogenic	Ambiguous	0.212	Likely Benign										-0.87	Neutral	0.264	Benign	0.102	Benign	4.20	Benign	0.53	Tolerated	4.32	2	2	0	1.0	-34.02
c.292C>G	H98D					6-33425900-C-G	1	6.20e-7	-1.739	Likely Benign	0.167	Likely Benign	Likely Benign	0.140	Likely Benign										-0.42	Neutral	0.115	Benign	0.012	Benign	4.24	Benign	0.00	Affected	4.32	1	-1	1	-0.3	-22.05
c.2932C>T	P978S		Uncertain		1				-3.913	Likely Benign	0.151	Likely Benign	Likely Benign	0.085	Likely Benign										-1.07	Neutral	0.481	Possibly Damaging	0.220	Benign	4.22	Benign	0.48	Tolerated			1	-1	0.8	-10.04
c.2935T>C	F979L		Uncertain		1				-2.341	Likely Benign	0.870	Likely Pathogenic	Ambiguous	0.228	Likely Benign										-1.00	Neutral	0.625	Possibly Damaging	0.430	Benign	4.22	Benign	0.73	Tolerated	4.32	2	2	0	1.0	-34.02
c.2939A>G	H980R					6-33443491-A-G	1	6.20e-7	-2.736	Likely Benign	0.409	Ambiguous	Likely Benign	0.095	Likely Benign										-1.44	Neutral	0.802	Possibly Damaging	0.354	Benign	4.17	Benign	0.00	Affected	4.32	1	0	2	-1.3	19.05
c.293A>T	H98L					6-33425901-A-T	1	6.32e-7	-1.804	Likely Benign	0.113	Likely Benign	Likely Benign	0.194	Likely Benign										-0.51	Neutral	0.115	Benign	0.012	Benign	4.24	Benign	0.00	Affected	4.32	1	-3	-2	7.0	-23.98
c.2945A>G	Y982C		Likely Benign		1	6-33443497-A-G	2	1.24e-6	-6.256	Likely Benign	0.746	Likely Pathogenic	Likely Benign	0.195	Likely Benign										-1.67	Neutral	0.997	Probably Damaging	0.923	Probably Damaging	3.87	Benign	0.00	Affected	4.32	1	0	-2	3.8	-60.04
c.2948G>A	S983N		Likely Benign		1	6-33443500-G-A	6	3.72e-6	-5.604	Likely Benign	0.909	Likely Pathogenic	Ambiguous	0.136	Likely Benign										-1.78	Neutral	0.991	Probably Damaging	0.988	Probably Damaging	2.04	Pathogenic	0.00	Affected	4.32	1	1	1	-2.7	27.03
c.2951A>G	K984R					6-33443503-A-G	2	1.24e-6	-2.044	Likely Benign	0.104	Likely Benign	Likely Benign	0.082	Likely Benign										-0.41	Neutral	0.012	Benign	0.012	Benign	2.67	Benign	0.00	Affected	4.32	1	2	3	-0.6	28.01
c.2952G>C	K984N					6-33443504-G-C	1	6.20e-7	-3.020	Likely Benign	0.955	Likely Pathogenic	Ambiguous	0.091	Likely Benign										0.52	Neutral	0.951	Possibly Damaging	0.637	Possibly Damaging	2.89	Benign	0.00	Affected	4.32	1	0	1	0.4	-14.07
c.2954G>A	S985N		Uncertain		1				-6.979	Likely Benign	0.845	Likely Pathogenic	Ambiguous	0.088	Likely Benign										-1.68	Neutral	0.991	Probably Damaging	0.988	Probably Damaging	2.65	Benign	0.00	Affected	4.32	1	1	1	-2.7	27.03
c.295G>C	E99Q					6-33425903-G-C	1	6.20e-7	-3.675	Likely Benign	0.325	Likely Benign	Likely Benign	0.056	Likely Benign										-0.82	Neutral	0.001	Benign	0.000	Benign	4.10	Benign	0.00	Affected	4.32	1	2	2	0.0	-0.98
c.2960A>G	D987G		Uncertain		1				-4.782	Likely Benign	0.849	Likely Pathogenic	Ambiguous	0.234	Likely Benign										-2.79	Deleterious	0.943	Possibly Damaging	0.808	Possibly Damaging	2.45	Pathogenic	0.07	Tolerated	4.32	2	1	-1	3.1	-58.04
c.2961C>A	D987E					6-33443513-C-A	1	6.20e-7	-4.406	Likely Benign	0.425	Ambiguous	Likely Benign	0.124	Likely Benign										-1.36	Neutral	0.049	Benign	0.044	Benign	2.64	Benign	0.04	Affected	4.32	2	2	3	0.0	14.03
c.2962C>T	L988F		Uncertain		1	6-33443514-C-T	1	6.20e-7	-4.368	Likely Benign	0.355	Ambiguous	Likely Benign	0.135	Likely Benign										-1.70	Neutral	0.977	Probably Damaging	0.900	Possibly Damaging	2.69	Benign	0.00	Affected	4.32	2	2	0	-1.0	34.02
c.2971G>A	G991R		Uncertain		3	6-33443523-G-A	8	4.96e-6	-3.934	Likely Benign	0.411	Ambiguous	Likely Benign	0.102	Likely Benign										-1.20	Neutral	0.984	Probably Damaging	0.772	Possibly Damaging	4.11	Benign	0.01	Affected	4.32	2	-3	-2	-4.1	99.14
c.2972G>C	G991A					6-33443524-G-C	1	6.20e-7	-3.585	Likely Benign	0.072	Likely Benign	Likely Benign	0.064	Likely Benign										-0.83	Neutral	0.002	Benign	0.026	Benign	4.20	Benign	0.62	Tolerated	4.32	2	0	1	2.2	14.03
c.2974G>A	V992I					6-33443526-G-A	5	3.10e-6	-3.851	Likely Benign	0.074	Likely Benign	Likely Benign	0.052	Likely Benign										-0.30	Neutral	0.302	Benign	0.089	Benign	4.20	Benign	0.29	Tolerated	4.32	2	3	4	0.3	14.03
c.2977C>T	P993S					6-33443529-C-T	3	1.86e-6	-3.665	Likely Benign	0.068	Likely Benign	Likely Benign	0.054	Likely Benign										-0.13	Neutral	0.011	Benign	0.023	Benign	4.26	Benign	0.59	Tolerated	4.32	2	-1	1	0.8	-10.04
c.2980A>G	K994E					6-33443532-A-G	1	6.20e-7	-2.587	Likely Benign	0.339	Likely Benign	Likely Benign	0.057	Likely Benign										-0.58	Neutral	0.036	Benign	0.039	Benign	4.14	Benign	0.02	Affected	4.32	2	1	0	0.4	0.94
c.2983C>T	P995S		Uncertain		1				-4.457	Likely Benign	0.071	Likely Benign	Likely Benign	0.042	Likely Benign										-1.03	Neutral	0.011	Benign	0.015	Benign	4.24	Benign	0.00	Affected	4.32	1	1	-1	0.8	-10.04
c.2986C>T	P996S					6-33443538-C-T	4	2.48e-6	-4.461	Likely Benign	0.063	Likely Benign	Likely Benign	0.064	Likely Benign										-0.58	Neutral	0.002	Benign	0.004	Benign	4.30	Benign	0.09	Tolerated	4.32	4	-1	1	0.8	-10.04
c.2987C>G	P996R		Uncertain		1				-4.457	Likely Benign	0.141	Likely Benign	Likely Benign	0.040	Likely Benign										-1.04	Neutral	0.144	Benign	0.085	Benign	4.26	Benign	0.01	Affected	4.32	4	-2	0	-2.9	59.07
c.2989G>A	A997T		Uncertain		1				-4.102	Likely Benign	0.071	Likely Benign	Likely Benign	0.085	Likely Benign										-0.62	Neutral	0.224	Benign	0.120	Benign	4.17	Benign	0.00	Affected	4.32	4	1	0	-2.5	30.03
c.298T>C	Y100H					6-33432163-T-C	1	6.20e-7	-2.094	Likely Benign	0.201	Likely Benign	Likely Benign	0.123	Likely Benign										-0.40	Neutral	0.978	Probably Damaging	0.500	Possibly Damaging	4.23	Benign	0.00	Affected	4.32	1	2	0	-1.9	-26.03
c.2998A>G	I1000V		Uncertain		2				-4.102	Likely Benign	0.098	Likely Benign	Likely Benign	0.086	Likely Benign										-0.20	Neutral	0.437	Benign	0.170	Benign	2.76	Benign	0.81	Tolerated	4.32	4	3	4	-0.3	-14.03
c.29G>A	R10Q		Uncertain		2	6-33420293-G-A	20	1.30e-5	-4.438	Likely Benign	0.185	Likely Benign	Likely Benign	0.084	Likely Benign										0.03	Neutral	0.121	Benign	0.004	Benign	4.17	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06
c.29G>C	R10P		Uncertain		2	6-33420293-G-C	2	1.30e-6	-3.772	Likely Benign	0.162	Likely Benign	Likely Benign	0.220	Likely Benign										-0.05	Neutral	0.233	Benign	0.026	Benign	4.13	Benign	0.00	Affected	4.32	1	0	-2	2.9	-59.07
c.3002T>C	L1001P		Uncertain		1				-3.071	Likely Benign	0.208	Likely Benign	Likely Benign	0.113	Likely Benign										-1.02	Neutral	0.966	Probably Damaging	0.690	Possibly Damaging	2.65	Benign	0.00	Affected	4.32	4	-3	-3	-5.4	-16.04
c.3005A>G	H1002R					6-33443557-A-G	1	6.20e-7	-3.624	Likely Benign	0.609	Likely Pathogenic	Likely Benign	0.082	Likely Benign										-1.52	Neutral	0.012	Benign	0.022	Benign	2.76	Benign	0.25	Tolerated	4.32	4	0	2	-1.3	19.05
c.3007A>G	S1003G					6-33443559-A-G	1	6.20e-7	-5.888	Likely Benign	0.542	Ambiguous	Likely Benign	0.088	Likely Benign										-1.72	Neutral	0.992	Probably Damaging	0.987	Probably Damaging	2.48	Pathogenic	0.00	Affected	3.77	5	0	1	0.4	-30.03
c.3009C>G	S1003R		Uncertain		1				-5.113	Likely Benign	0.991	Likely Pathogenic	Likely Pathogenic	0.141	Likely Benign										-1.88	Neutral	0.999	Probably Damaging	0.996	Probably Damaging	2.48	Pathogenic	0.00	Affected	3.77	5	0	-1	-3.7	69.11
c.3012C>G	H1004Q					6-33443564-C-G	3	1.86e-6	-3.872	Likely Benign	0.853	Likely Pathogenic	Ambiguous	0.126	Likely Benign										-1.55	Neutral	0.999	Probably Damaging	0.996	Probably Damaging	2.78	Benign	0.71	Tolerated	3.77	5	0	3	-0.3	-9.01
c.3013A>G	S1005G					6-33443565-A-G			-6.785	Likely Benign	0.537	Ambiguous	Likely Benign	0.095	Likely Benign										-1.98	Neutral	0.992	Probably Damaging	0.987	Probably Damaging	2.63	Benign	0.00	Affected	3.77	5	0	1	0.4	-30.03
c.3014G>A	S1005N					6-33443566-G-A	1	6.20e-7	-6.577	Likely Benign	0.890	Likely Pathogenic	Ambiguous	0.110	Likely Benign										-1.50	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.65	Benign	0.00	Affected	3.77	5	1	1	-2.7	27.03
c.3015C>G	S1005R					6-33443567-C-G	2	1.24e-6	-3.300	Likely Benign	0.993	Likely Pathogenic	Likely Pathogenic	0.165	Likely Benign										-2.29	Neutral	0.999	Probably Damaging	0.996	Probably Damaging	2.66	Benign	0.00	Affected	3.77	5	-1	0	-3.7	69.11
c.3016T>G	Y1006D					6-33443568-T-G			-5.296	Likely Benign	0.898	Likely Pathogenic	Ambiguous	0.196	Likely Benign										-1.53	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	2.73	Benign	0.56	Tolerated	3.77	5	-3	-4	-2.2	-48.09
c.3020G>A	S1007N		Benign		1				-5.113	Likely Benign	0.803	Likely Pathogenic	Ambiguous	0.075	Likely Benign										-1.54	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.65	Benign	0.01	Affected	3.77	5	1	1	-2.7	27.03
c.3020G>C	S1007T					6-33443572-G-C			-4.719	Likely Benign	0.303	Likely Benign	Likely Benign	0.071	Likely Benign										-1.24	Neutral	0.992	Probably Damaging	0.987	Probably Damaging	2.68	Benign	0.03	Affected	3.77	5	1	1	0.1	14.03
c.3022G>A	D1008N		Likely Benign		1	6-33443574-G-A	3	1.86e-6	-4.045	Likely Benign	0.714	Likely Pathogenic	Likely Benign	0.128	Likely Benign										-2.15	Neutral	0.999	Probably Damaging	0.997	Probably Damaging	2.75	Benign	0.01	Affected	3.77	5	2	1	0.0	-0.98
c.3022G>C	D1008H					6-33443574-G-C	1	6.20e-7	-3.612	Likely Benign	0.915	Likely Pathogenic	Ambiguous	0.213	Likely Benign										-2.46	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	2.64	Benign	0.01	Affected	3.77	5	-1	1	0.3	22.05
c.3023A>G	D1008G		Uncertain		1	6-33443575-A-G	1	6.20e-7	-3.213	Likely Benign	0.742	Likely Pathogenic	Likely Benign	0.203	Likely Benign										-2.84	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	2.65	Benign	0.01	Affected	3.77	5	-1	1	3.1	-58.04
c.3024T>A	D1008E					6-33443576-T-A	1	6.20e-7	-2.809	Likely Benign	0.428	Ambiguous	Likely Benign	0.151	Likely Benign										-0.53	Neutral	0.997	Probably Damaging	0.994	Probably Damaging	2.93	Benign	1.00	Tolerated	3.77	5	2	3	0.0	14.03
c.3024T>G	D1008E					6-33443576-T-G			-2.809	Likely Benign	0.428	Ambiguous	Likely Benign	0.151	Likely Benign										-0.53	Neutral	0.997	Probably Damaging	0.994	Probably Damaging	2.93	Benign	1.00	Tolerated	3.77	5	2	3	0.0	14.03
c.3025G>C	E1009Q					6-33443577-G-C	1	6.20e-7	-3.423	Likely Benign	0.615	Likely Pathogenic	Likely Benign	0.057	Likely Benign										-1.65	Neutral	0.980	Probably Damaging	0.782	Possibly Damaging	2.39	Pathogenic	0.02	Affected	3.77	5	2	2	0.0	-0.98
c.3026A>C	E1009A		Uncertain		1				-3.118	Likely Benign	0.679	Likely Pathogenic	Likely Benign	0.109	Likely Benign										-3.06	Deleterious	0.980	Probably Damaging	0.630	Possibly Damaging	2.39	Pathogenic	0.01	Affected	3.77	5	0	-1	5.3	-58.04
c.3027G>C	E1009D					6-33443579-G-C	1	6.20e-7	-2.958	Likely Benign	0.104	Likely Benign	Likely Benign	0.054	Likely Benign										-0.37	Neutral	0.011	Benign	0.017	Benign	2.50	Benign	0.30	Tolerated	3.77	5	2	3	0.0	-14.03
c.3029T>C	F1010S					6-33443581-T-C			-1.722	Likely Benign	0.744	Likely Pathogenic	Likely Benign	0.153	Likely Benign										-1.97	Neutral	0.994	Probably Damaging	0.892	Possibly Damaging	2.51	Benign	0.01	Affected	3.77	5	-2	-3	-3.6	-60.10
c.3031G>A	G1011R					6-33443583-G-A			-4.650	Likely Benign	0.609	Likely Pathogenic	Likely Benign	0.118	Likely Benign										-0.79	Neutral	0.642	Possibly Damaging	0.494	Possibly Damaging	2.72	Benign	0.01	Affected	3.77	5	-2	-3	-4.1	99.14
c.3032G>C	G1011A					6-33443584-G-C			-4.349	Likely Benign	0.097	Likely Benign	Likely Benign	0.077	Likely Benign										-0.04	Neutral	0.139	Benign	0.089	Benign	2.89	Benign	0.64	Tolerated	3.77	5	0	1	2.2	14.03
c.3034C>T	P1012S					6-33443586-C-T	2	1.24e-6	-3.342	Likely Benign	0.087	Likely Benign	Likely Benign	0.044	Likely Benign										-0.23	Neutral	0.224	Benign	0.131	Benign	2.81	Benign	0.22	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3037T>C	S1013P					6-33443589-T-C	2	1.24e-6	-2.563	Likely Benign	0.103	Likely Benign	Likely Benign	0.103	Likely Benign										-1.27	Neutral	0.453	Possibly Damaging	0.150	Benign	2.66	Benign	0.15	Tolerated	3.77	5	-1	1	-0.8	10.04
c.3038C>G	S1013C		Uncertain		1	6-33443590-C-G	4	2.48e-6	-6.745	Likely Benign	0.110	Likely Benign	Likely Benign	0.058	Likely Benign										-2.06	Neutral	0.898	Possibly Damaging	0.579	Possibly Damaging	2.64	Benign	0.05	Affected	3.77	5	0	-1	3.3	16.06
c.3038C>T	S1013F					6-33443590-C-T	1	6.20e-7	-5.370	Likely Benign	0.353	Ambiguous	Likely Benign	0.057	Likely Benign										-2.54	Deleterious	0.453	Possibly Damaging	0.272	Benign	2.65	Benign	0.03	Affected	3.77	5	-2	-3	3.6	60.10
c.303C>A	H101Q		Uncertain		1	6-33432168-C-A	1	6.20e-7	-2.827	Likely Benign	0.124	Likely Benign	Likely Benign	0.147	Likely Benign										-0.37	Neutral	0.824	Possibly Damaging	0.880	Possibly Damaging	4.24	Benign	0.00	Affected	4.32	1	3	0	-0.3	-9.01
c.3041G>A	G1014D					6-33443593-G-A			-4.462	Likely Benign	0.543	Ambiguous	Likely Benign	0.029	Likely Benign										-1.39	Neutral	0.818	Possibly Damaging	0.381	Benign	2.74	Benign	0.77	Tolerated	3.77	5	-1	1	-3.1	58.04
c.3041G>T	G1014V		Uncertain		1				-4.612	Likely Benign	0.181	Likely Benign	Likely Benign	0.053	Likely Benign										-2.47	Neutral	0.818	Possibly Damaging	0.377	Benign	2.72	Benign	0.06	Tolerated	3.77	5	-1	-3	4.6	42.08
c.3046G>C	D1016H					6-33443598-G-C			-3.398	Likely Benign	0.792	Likely Pathogenic	Ambiguous	0.259	Likely Benign										-2.63	Deleterious	0.994	Probably Damaging	0.924	Probably Damaging	2.45	Pathogenic	0.00	Affected	3.77	5	-1	1	0.3	22.05
c.3048C>A	D1016E					6-33443600-C-A	2	1.24e-6	-3.422	Likely Benign	0.216	Likely Benign	Likely Benign	0.017	Likely Benign										-0.37	Neutral	0.008	Benign	0.028	Benign	2.64	Benign	0.65	Tolerated	3.77	5	2	3	0.0	14.03
c.304T>G	L102V		Uncertain		1	6-33432169-T-G	1	6.20e-7	-4.316	Likely Benign	0.068	Likely Benign	Likely Benign	0.102	Likely Benign										0.32	Neutral	0.880	Possibly Damaging	0.899	Possibly Damaging	4.21	Benign	0.00	Affected	4.32	1	2	1	0.4	-14.03
c.3050T>A	F1017Y					6-33443602-T-A			-3.583	Likely Benign	0.185	Likely Benign	Likely Benign	0.042	Likely Benign										-0.75	Neutral	0.012	Benign	0.044	Benign	2.47	Pathogenic	0.05	Affected	3.77	5	3	7	-4.1	16.00
c.3051C>A	F1017L					6-33443603-C-A			-2.048	Likely Benign	0.934	Likely Pathogenic	Ambiguous	0.140	Likely Benign										-2.38	Neutral	0.798	Possibly Damaging	0.373	Benign	2.65	Benign	0.72	Tolerated	3.77	5	0	2	1.0	-34.02
c.3053C>T	T1018I		Uncertain		1	6-33443605-C-T	4	2.48e-6	-3.264	Likely Benign	0.524	Ambiguous	Likely Benign	0.076	Likely Benign										-2.55	Deleterious	0.586	Possibly Damaging	0.304	Benign	2.24	Pathogenic	0.01	Affected	3.77	5	-1	0	5.2	12.05
c.3055C>T	R1019C		Conflicting		2	6-33443607-C-T	10	6.19e-6	-7.386	In-Between	0.646	Likely Pathogenic	Likely Benign	0.168	Likely Benign										-4.00	Deleterious	0.999	Probably Damaging	0.880	Possibly Damaging	2.36	Pathogenic	0.00	Affected	3.77	5	-4	-3	7.0	-53.05																10.1016/j.ajhg.2020.11.011
c.3056G>A	R1019H		Conflicting		2	6-33443608-G-A	67	4.15e-5	-4.610	Likely Benign	0.258	Likely Benign	Likely Benign	0.122	Likely Benign										-1.95	Neutral	0.995	Probably Damaging	0.845	Possibly Damaging	2.39	Pathogenic	0.01	Affected	3.77	5	2	0	1.3	-19.05
c.3056G>T	R1019L		Uncertain		1	6-33443608-G-T	2	1.24e-6	-5.194	Likely Benign	0.752	Likely Pathogenic	Likely Benign	0.110	Likely Benign										-3.57	Deleterious	0.800	Possibly Damaging	0.573	Possibly Damaging	2.40	Pathogenic	0.01	Affected	3.77	5	-2	-3	8.3	-43.03
c.3058C>T	R1020W					6-33443610-C-T	6	3.72e-6	-9.378	Likely Pathogenic	0.829	Likely Pathogenic	Ambiguous	0.165	Likely Benign										-4.14	Deleterious	1.000	Probably Damaging	0.986	Probably Damaging	2.44	Pathogenic	0.00	Affected	3.77	5	-3	2	3.6	30.03
c.3059G>A	R1020Q					6-33443611-G-A	2	1.24e-6	-3.753	Likely Benign	0.445	Ambiguous	Likely Benign	0.137	Likely Benign										-2.19	Neutral	0.995	Probably Damaging	0.870	Possibly Damaging	2.52	Benign	0.00	Affected	3.77	5	1	1	1.0	-28.06
c.3059G>T	R1020L		Uncertain		1				-6.031	Likely Benign	0.907	Likely Pathogenic	Ambiguous	0.216	Likely Benign										-4.03	Deleterious	0.990	Probably Damaging	0.921	Probably Damaging	2.50	Benign	0.00	Affected	3.77	5	-3	-2	8.3	-43.03
c.3062A>G	Q1021R					6-33443614-A-G	1	6.20e-7	-4.467	Likely Benign	0.770	Likely Pathogenic	Likely Benign	0.174	Likely Benign										-1.80	Neutral	0.985	Probably Damaging	0.982	Probably Damaging	2.61	Benign	0.03	Affected	3.77	5	1	1	-1.0	28.06
c.3064C>T	L1022F					6-33443616-C-T	2	1.24e-6	-5.035	Likely Benign	0.351	Ambiguous	Likely Benign	0.072	Likely Benign										-1.84	Neutral	0.971	Probably Damaging	0.801	Possibly Damaging	2.51	Benign	0.07	Tolerated	3.77	5	0	2	-1.0	34.02
c.3067T>C	S1023P					6-33443619-T-C	2	1.24e-6	-5.634	Likely Benign	0.679	Likely Pathogenic	Likely Benign	0.146	Likely Benign										-2.11	Neutral	0.997	Probably Damaging	0.995	Probably Damaging	2.43	Pathogenic	0.02	Affected	3.77	5	-1	1	-0.8	10.04
c.3076G>C	D1026H					6-33443628-G-C	1	6.20e-7	-4.412	Likely Benign	0.900	Likely Pathogenic	Ambiguous	0.105	Likely Benign										-2.03	Neutral	0.832	Possibly Damaging	0.600	Possibly Damaging	2.48	Pathogenic	0.00	Affected	3.77	5	-1	1	0.3	22.05
c.3085C>G	Q1029E					6-33443637-C-G	17	1.05e-5	-3.660	Likely Benign	0.281	Likely Benign	Likely Benign	0.044	Likely Benign										-0.92	Neutral	0.625	Possibly Damaging	0.258	Benign	2.83	Benign	0.26	Tolerated	3.77	5	2	2	0.0	0.98
c.3088C>G	H1030D					6-33443640-C-G	1	6.19e-7	-3.500	Likely Benign	0.424	Ambiguous	Likely Benign	0.189	Likely Benign										-0.85	Neutral	0.126	Benign	0.066	Benign	2.78	Benign	0.05	Affected	3.77	5	-1	1	-0.3	-22.05
c.3091A>G	M1031V					6-33443643-A-G	7	4.34e-6	-2.815	Likely Benign	0.198	Likely Benign	Likely Benign	0.054	Likely Benign										-0.81	Neutral	0.002	Benign	0.003	Benign	2.72	Benign	0.44	Tolerated	3.77	5	1	2	2.3	-32.06
c.3092T>C	M1031T		Uncertain		1	6-33443644-T-C	2	1.24e-6	-1.863	Likely Benign	0.540	Ambiguous	Likely Benign	0.085	Likely Benign										-0.24	Neutral	0.002	Benign	0.005	Benign	2.67	Benign	1.00	Tolerated	3.77	5	-1	-1	-2.6	-30.09
c.3098C>A	S1033Y					6-33443650-C-A	1	6.19e-7	-4.857	Likely Benign	0.564	Ambiguous	Likely Benign	0.034	Likely Benign										-1.01	Neutral	0.021	Benign	0.008	Benign	2.69	Benign	0.04	Affected	3.77	5	-2	-3	-0.5	76.10
c.3100C>G	P1034A		Benign		1				-4.174	Likely Benign	0.178	Likely Benign	Likely Benign	0.060	Likely Benign										-2.44	Neutral	0.059	Benign	0.061	Benign	2.47	Pathogenic	0.06	Tolerated	3.77	5	1	-1	3.4	-26.04
c.3103C>A	P1035T		Uncertain		1				-4.447	Likely Benign	0.426	Ambiguous	Likely Benign	0.087	Likely Benign										-0.96	Neutral	0.901	Possibly Damaging	0.537	Possibly Damaging	2.72	Benign	0.23	Tolerated	3.77	5	0	-1	0.9	3.99
c.3108G>T	Q1036H					6-33443660-G-T	1	6.20e-7	-4.189	Likely Benign	0.536	Ambiguous	Likely Benign	0.065	Likely Benign										-1.18	Neutral	0.977	Probably Damaging	0.615	Possibly Damaging	2.50	Benign	0.29	Tolerated	3.77	5	0	3	0.3	9.01
c.310C>T	R104C					6-33432175-C-T	2	1.24e-6	-5.716	Likely Benign	0.475	Ambiguous	Likely Benign	0.109	Likely Benign										-1.41	Neutral	0.993	Probably Damaging	0.446	Benign	3.99	Benign	0.00	Affected	4.32	1	-3	-4	7.0	-53.05																10.1016/j.ajhg.2020.11.011
c.3110T>C	I1037T					6-33443662-T-C	1	6.21e-7	-2.565	Likely Benign	0.973	Likely Pathogenic	Likely Pathogenic	0.066	Likely Benign										0.40	Neutral	0.292	Benign	0.110	Benign	2.79	Benign	0.34	Tolerated	3.77	5	-1	0	-5.2	-12.05
c.3116T>C	I1039T					6-33443668-T-C	12	7.43e-6	-2.465	Likely Benign	0.645	Likely Pathogenic	Likely Benign	0.193	Likely Benign										0.45	Neutral	0.004	Benign	0.008	Benign	2.75	Benign	0.10	Tolerated	3.77	5	-1	0	-5.2	-12.05
c.3119G>T	G1040V		Uncertain		1	6-33443671-G-T	4	2.48e-6	-3.453	Likely Benign	0.645	Likely Pathogenic	Likely Benign	0.774	Likely Pathogenic										-2.89	Deleterious	0.827	Possibly Damaging	0.456	Possibly Damaging	-0.74	Pathogenic	0.01	Affected	3.77	5	-1	-3	4.6	42.08
c.311G>A	R104H					6-33432176-G-A	2	1.24e-6	-4.126	Likely Benign	0.268	Likely Benign	Likely Benign	0.094	Likely Benign										-1.42	Neutral	0.066	Benign	0.004	Benign	4.02	Benign	0.00	Affected	4.32	1	0	2	1.3	-19.05
c.311G>T	R104L		Benign		1	6-33432176-G-T	1	6.20e-7	-3.563	Likely Benign	0.578	Likely Pathogenic	Likely Benign	0.170	Likely Benign										-1.38	Neutral	0.001	Benign	0.002	Benign	4.05	Benign	0.00	Affected	4.32	1	-2	-3	8.3	-43.03
c.3121C>T	P1041S		Conflicting		2	6-33443673-C-T	1	6.20e-7	-4.246	Likely Benign	0.121	Likely Benign	Likely Benign	0.344	Likely Benign										-2.72	Deleterious	0.664	Possibly Damaging	0.283	Benign	5.48	Benign	0.11	Tolerated	3.77	5	1	-1	0.8	-10.04
c.3125A>G	Q1042R		Uncertain		2	6-33443677-A-G	2	1.24e-6	-2.928	Likely Benign	0.412	Ambiguous	Likely Benign	0.300	Likely Benign										-1.39	Neutral	0.586	Possibly Damaging	0.120	Benign	5.48	Benign	0.12	Tolerated	3.77	5	1	1	-1.0	28.06
c.3129G>T	R1043S					6-33443681-G-T	2	1.24e-6	-3.223	Likely Benign	0.457	Ambiguous	Likely Benign	0.509	Likely Pathogenic										-2.10	Neutral	0.036	Benign	0.018	Benign	5.42	Benign	0.00	Affected	3.77	5	-1	0	3.7	-69.11
c.3130C>A	P1044T					6-33443682-C-A	1	6.20e-7	-4.605	Likely Benign	0.075	Likely Benign	Likely Benign	0.372	Likely Benign										-1.02	Neutral	0.126	Benign	0.096	Benign	5.53	Benign	0.17	Tolerated	3.77	5	-1	0	0.9	3.99
c.3134C>G	A1045G		Benign/Likely benign		7	6-33443686-C-G	1407	8.72e-4	-3.246	Likely Benign	0.075	Likely Benign	Likely Benign	0.024	Likely Benign										-1.21	Neutral	0.224	Benign	0.066	Benign	2.64	Benign	0.33	Tolerated	3.77	5	1	0	-2.2	-14.03																10.1016/j.ajhg.2020.11.011
c.3136C>G	P1046A		Uncertain		1	6-33443688-C-G	1	6.20e-7	-3.246	Likely Benign	0.048	Likely Benign	Likely Benign	0.041	Likely Benign										-1.67	Neutral	0.001	Benign	0.008	Benign	2.39	Pathogenic	0.29	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3137C>T	P1046L					6-33443689-C-T	1	6.20e-7	-5.022	Likely Benign	0.116	Likely Benign	Likely Benign	0.100	Likely Benign										-2.11	Neutral	0.001	Benign	0.005	Benign	2.35	Pathogenic	0.05	Affected	3.77	5	-3	-3	5.4	16.04
c.313T>C	S105P		Uncertain		1				-3.631	Likely Benign	0.166	Likely Benign	Likely Benign	0.204	Likely Benign										0.03	Neutral	0.808	Possibly Damaging	0.212	Benign	4.00	Benign	0.00	Affected	4.32	1	-1	1	-0.8	10.04
c.3140C>T	S1047L					6-33443692-C-T	1	6.20e-7	-4.062	Likely Benign	0.132	Likely Benign	Likely Benign	0.032	Likely Benign										-0.63	Neutral	0.144	Benign	0.058	Benign	2.60	Benign	0.02	Affected	3.77	5	-2	-3	4.6	26.08
c.3142G>C	G1048R		Uncertain		1				-4.305	Likely Benign	0.435	Ambiguous	Likely Benign	0.503	Likely Pathogenic										-0.54	Neutral	0.919	Possibly Damaging	0.728	Possibly Damaging	2.54	Benign	0.10	Tolerated	3.77	5	-2	-3	-4.1	99.14
c.3145C>T	P1049S					6-33443697-C-T	2	1.24e-6	-2.351	Likely Benign	0.053	Likely Benign	Likely Benign	0.071	Likely Benign										-1.53	Neutral	0.519	Possibly Damaging	0.303	Benign	2.76	Benign	0.04	Affected	3.77	5	-1	1	0.8	-10.04
c.3148G>A	G1050R					6-33443700-G-A	3	1.86e-6	-6.637	Likely Benign	0.349	Ambiguous	Likely Benign	0.045	Likely Benign										-0.68	Neutral	0.009	Benign	0.008	Benign	2.48	Pathogenic	0.06	Tolerated	3.77	5	-2	-3	-4.1	99.14
c.314C>G	S105W					6-33432179-C-G	2	1.24e-6	-5.600	Likely Benign	0.606	Likely Pathogenic	Likely Benign	0.177	Likely Benign										-2.28	Neutral	0.998	Probably Damaging	0.844	Possibly Damaging	3.97	Benign	0.00	Affected	4.32	1	-3	-2	-0.1	99.14
c.314C>T	S105L		Uncertain		2	6-33432179-C-T	4	2.48e-6	-3.710	Likely Benign	0.233	Likely Benign	Likely Benign	0.095	Likely Benign										-1.52	Neutral	0.828	Possibly Damaging	0.048	Benign	4.06	Benign	0.00	Affected	4.32	1	-3	-2	4.6	26.08
c.3151G>T	G1051C		Likely Pathogenic		1				-9.050	Likely Pathogenic	0.122	Likely Benign	Likely Benign	0.497	Likely Benign										-0.90	Neutral	0.971	Probably Damaging	0.750	Possibly Damaging	-0.74	Pathogenic	0.10	Tolerated	3.77	5	-3	-3	2.9	46.09
c.3152G>A	G1051D					6-33443704-G-A	2	1.24e-6	-9.379	Likely Pathogenic	0.311	Likely Benign	Likely Benign	0.445	Likely Benign										-0.31	Neutral	0.761	Possibly Damaging	0.239	Benign	-0.74	Pathogenic	0.39	Tolerated	3.77	5	-1	1	-3.1	58.04
c.3152G>T	G1051V					6-33443704-G-T	1	6.20e-7	-7.098	In-Between	0.102	Likely Benign	Likely Benign	0.460	Likely Benign										-0.62	Neutral	0.245	Benign	0.096	Benign	-0.74	Pathogenic	0.17	Tolerated	3.77	5	-3	-1	4.6	42.08
c.3154G>A	G1052R		Uncertain		1				-9.050	Likely Pathogenic	0.383	Ambiguous	Likely Benign	0.497	Likely Benign										-0.41	Neutral	0.990	Probably Damaging	0.798	Possibly Damaging	3.90	Benign	0.10	Tolerated	3.77	5	-2	-3	-4.1	99.14
c.3157A>T	S1053C					6-33443709-A-T			-7.574	In-Between	0.095	Likely Benign	Likely Benign	0.220	Likely Benign										-0.61	Neutral	0.977	Probably Damaging	0.777	Possibly Damaging	5.30	Benign	0.11	Tolerated	3.77	5	-1	0	3.3	16.06
c.3158G>A	S1053N					6-33443710-G-A	1	6.21e-7	-6.282	Likely Benign	0.120	Likely Benign	Likely Benign	0.208	Likely Benign										-0.54	Neutral	0.625	Possibly Damaging	0.193	Benign	5.30	Benign	0.34	Tolerated	3.77	5	1	1	-2.7	27.03
c.3159C>A	S1053R					6-33443711-C-A	1	1.10e-6	-6.421	Likely Benign	0.359	Ambiguous	Likely Benign	0.303	Likely Benign										0.43	Neutral	0.969	Probably Damaging	0.581	Possibly Damaging	5.33	Benign	0.59	Tolerated	3.77	5	-1	0	-3.7	69.11
c.3159C>G	S1053R					6-33443711-C-G			-6.421	Likely Benign	0.359	Ambiguous	Likely Benign	0.304	Likely Benign										0.43	Neutral	0.969	Probably Damaging	0.581	Possibly Damaging	5.33	Benign	0.59	Tolerated	3.77	5	-1	0	-3.7	69.11
c.3160G>A	G1054S		Benign		1	6-33443712-G-A	32	1.99e-5	-5.294	Likely Benign	0.075	Likely Benign	Likely Benign	0.160	Likely Benign										0.21	Neutral	0.121	Benign	0.013	Benign	4.04	Benign	0.63	Tolerated	3.77	5	1	0	-0.4	30.03
c.3161G>A	G1054D		Uncertain		1				-10.385	Likely Pathogenic	0.351	Ambiguous	Likely Benign	0.279	Likely Benign										-0.26	Neutral	0.818	Possibly Damaging	0.266	Benign	4.07	Benign	0.37	Tolerated	3.77	5	1	-1	-3.1	58.04
c.3161G>C	G1054A					6-33443713-G-C			-6.786	Likely Benign	0.078	Likely Benign	Likely Benign	0.243	Likely Benign										-0.05	Neutral	0.288	Benign	0.071	Benign	4.03	Benign	1.00	Tolerated	3.77	5	0	1	2.2	14.03
c.3164G>A	G1055E					6-33443716-G-A	1	6.21e-7	-10.951	Likely Pathogenic	0.290	Likely Benign	Likely Benign	0.320	Likely Benign										-0.03	Neutral	0.901	Possibly Damaging	0.456	Possibly Damaging	3.30	Benign	0.10	Tolerated	3.77	5	-2	0	-3.1	72.06
c.3169A>C	S1057R					6-33443721-A-C			-6.648	Likely Benign	0.379	Ambiguous	Likely Benign	0.221	Likely Benign										-0.24	Neutral	0.677	Possibly Damaging	0.168	Benign	5.30	Benign	0.21	Tolerated	3.77	5	-1	0	-3.7	69.11
c.3169A>G	S1057G					6-33443721-A-G	1	7.20e-7	-1.005	Likely Benign	0.049	Likely Benign	Likely Benign	0.211	Likely Benign										-0.47	Neutral	0.421	Benign	0.111	Benign	5.76	Benign	0.52	Tolerated	3.77	5	0	1	0.4	-30.03
c.3169A>T	S1057C					6-33443721-A-T			-7.529	In-Between	0.100	Likely Benign	Likely Benign	0.258	Likely Benign										-0.64	Neutral	0.977	Probably Damaging	0.683	Possibly Damaging	5.23	Benign	0.10	Tolerated	3.77	5	-1	0	3.3	16.06
c.316A>G	R106G					6-33432181-A-G	1	6.20e-7	-2.617	Likely Benign	0.835	Likely Pathogenic	Ambiguous	0.161	Likely Benign										-2.21	Neutral	0.421	Benign	0.050	Benign	3.65	Benign	0.00	Affected	4.05	3	-2	-3	4.1	-99.14
c.3171C>G	S1057R					6-33443723-C-G			-6.648	Likely Benign	0.379	Ambiguous	Likely Benign	0.272	Likely Benign										-0.24	Neutral	0.677	Possibly Damaging	0.168	Benign	5.30	Benign	0.21	Tolerated	3.77	5	-1	0	-3.7	69.11
c.3172G>A	G1058S		Conflicting		3	6-33443724-G-A	114	7.08e-5	-5.178	Likely Benign	0.081	Likely Benign	Likely Benign	0.108	Likely Benign										0.26	Neutral	0.001	Benign	0.001	Benign	5.38	Benign	0.04	Affected	3.77	5	1	0	-0.4	30.03
c.3172G>T	G1058C					6-33443724-G-T	1	6.21e-7	-9.384	Likely Pathogenic	0.132	Likely Benign	Likely Benign	0.264	Likely Benign										-0.19	Neutral	0.600	Possibly Damaging	0.433	Benign	5.19	Benign	0.01	Affected	3.77	5	-3	-3	2.9	46.09
c.3173G>A	G1058D					6-33443725-G-A	1	6.21e-7	-10.344	Likely Pathogenic	0.391	Ambiguous	Likely Benign	0.177	Likely Benign										-0.33	Neutral	0.077	Benign	0.042	Benign	5.20	Benign	0.01	Affected	3.77	5	-1	1	-3.1	58.04
c.3173G>T	G1058V					6-33443725-G-T	1	6.21e-7	-6.877	Likely Benign	0.114	Likely Benign	Likely Benign	0.152	Likely Benign										-0.12	Neutral	0.000	Benign	0.001	Benign	5.22	Benign	0.01	Affected	3.77	5	-3	-1	4.6	42.08
c.3175G>A	G1059R		Uncertain		1	6-33443727-G-A	68	4.23e-5	-8.452	Likely Pathogenic	0.376	Ambiguous	Likely Benign	0.333	Likely Benign										-0.55	Neutral	0.001	Benign	0.001	Benign	2.53	Benign	0.00	Affected	4.32	2	-3	-2	-4.1	99.14
c.3176G>A	G1059E					6-33443728-G-A	1	6.22e-7	-10.459	Likely Pathogenic	0.296	Likely Benign	Likely Benign	0.390	Likely Benign										-0.71	Neutral	0.126	Benign	0.066	Benign	2.53	Benign	0.00	Affected	4.32	2	-2	0	-3.1	72.06
c.3176G>C	G1059A		Uncertain		1	6-33443728-G-C	4	2.49e-6	-6.754	Likely Benign	0.081	Likely Benign	Likely Benign	0.329	Likely Benign										-0.17	Neutral	0.001	Benign	0.002	Benign	2.56	Benign	0.00	Affected	4.32	2	1	0	2.2	14.03
c.3178G>A	G1060S		Uncertain		1	6-33443730-G-A			-4.759	Likely Benign	0.082	Likely Benign	Likely Benign	0.376	Likely Benign										-0.08	Neutral	0.271	Benign	0.054	Benign	2.69	Benign	0.49	Tolerated	4.32	2	1	0	-0.4	30.03
c.3179G>T	G1060V		Benign		1	6-33443731-G-T	1	6.22e-7	-6.966	Likely Benign	0.103	Likely Benign	Likely Benign	0.369	Likely Benign										-0.73	Neutral	0.986	Probably Damaging	0.728	Possibly Damaging	2.63	Benign	0.33	Tolerated	4.32	2	-1	-3	4.6	42.08
c.3181G>A	G1061S		Uncertain		1				-4.891	Likely Benign	0.079	Likely Benign	Likely Benign	0.283	Likely Benign										-0.68	Neutral	0.004	Benign	0.004	Benign	4.00	Benign	0.00	Affected			1	0	-0.4	30.03
c.3181G>T	G1061C		Conflicting		2	6-33443733-G-T	6	3.73e-6	-9.511	Likely Pathogenic	0.119	Likely Benign	Likely Benign	0.409	Likely Benign										-1.46	Neutral	0.938	Possibly Damaging	0.665	Possibly Damaging	3.97	Benign	0.00	Affected	4.32	2	-3	-3	2.9	46.09
c.3184G>A	G1062R		Uncertain		2	6-33443736-G-A	7	4.35e-6	-6.933	Likely Benign	0.353	Ambiguous	Likely Benign	0.403	Likely Benign										-0.34	Neutral	0.797	Possibly Damaging	0.139	Benign	4.10	Benign	0.01	Affected	4.32	2	-3	-2	-4.1	99.14
c.3192G>C	Q1064H		Uncertain		1				-4.576	Likely Benign	0.162	Likely Benign	Likely Benign	0.063	Likely Benign										-0.66	Neutral	0.938	Possibly Damaging	0.596	Possibly Damaging	4.15	Benign	0.05	Affected			3	0	0.3	9.01
c.3194C>T	P1065L		Likely Benign		1	6-33443746-C-T	14	8.71e-6	-5.085	Likely Benign	0.089	Likely Benign	Likely Benign	0.068	Likely Benign										-2.94	Deleterious	0.950	Possibly Damaging	0.419	Benign	2.01	Pathogenic	0.00	Affected	4.32	2	-3	-3	5.4	16.04
c.3196C>T	P1066S		Likely Pathogenic		1				-4.746	Likely Benign	0.070	Likely Benign	Likely Benign	0.145	Likely Benign										-2.47	Neutral	0.972	Probably Damaging	0.850	Possibly Damaging	2.74	Benign	0.00	Affected	4.32	2	1	-1	0.8	-10.04
c.3197C>T	P1066L		Uncertain		1	6-33443749-C-T	14	8.71e-6	-5.478	Likely Benign	0.092	Likely Benign	Likely Benign	0.173	Likely Benign										-3.68	Deleterious	0.996	Probably Damaging	0.903	Possibly Damaging	2.72	Benign	0.00	Affected	4.32	2	-3	-3	5.4	16.04
c.31G>A	G11R					6-33420295-G-A			-3.418	Likely Benign	0.427	Ambiguous	Likely Benign	0.102	Likely Benign										-0.47	Neutral	0.498	Possibly Damaging	0.026	Benign	3.92	Benign	0.00	Affected	4.32	1	-2	-3	-4.1	99.14
c.31G>T	G11W					6-33420295-G-T			-5.819	Likely Benign	0.403	Ambiguous	Likely Benign	0.096	Likely Benign										-0.67	Neutral	0.959	Probably Damaging	0.318	Benign	3.87	Benign	0.00	Affected	4.32	1	-2	-7	-0.5	129.16
c.3209G>A	R1070K		Conflicting		2				-5.093	Likely Benign	0.326	Likely Benign	Likely Benign	0.104	Likely Benign										-1.42	Neutral	0.049	Benign	0.048	Benign	3.86	Benign	0.09	Tolerated	3.77	5	3	2	0.6	-28.01
c.3209_3210delinsCA	R1070T		Uncertain		1				-5.093	Likely Benign	0.860	Likely Pathogenic	Ambiguous												-2.35	Neutral	0.948	Possibly Damaging	0.507	Possibly Damaging	3.78	Benign	0.01	Affected	3.77	5	-1	-1	3.8	-55.08
c.3212G>T	G1071V					6-33443764-G-T	3	1.87e-6	-2.901	Likely Benign	0.300	Likely Benign	Likely Benign	0.110	Likely Benign										-2.42	Neutral	0.057	Benign	0.022	Benign	4.14	Benign	0.01	Affected	3.77	5	-3	-1	4.6	42.08
c.3215A>G	K1072R					6-33443767-A-G	1	6.23e-7	-2.458	Likely Benign	0.100	Likely Benign	Likely Benign	0.116	Likely Benign										-0.15	Neutral	0.997	Probably Damaging	0.989	Probably Damaging	4.16	Benign	0.88	Tolerated	3.77	5	2	3	-0.6	28.01
c.3217T>C	S1073P					6-33443769-T-C	1	6.23e-7	-4.520	Likely Benign	0.338	Likely Benign	Likely Benign	0.082	Likely Benign										-0.76	Neutral	0.006	Benign	0.008	Benign	3.85	Benign	0.01	Affected	3.77	5	-1	1	-0.8	10.04
c.3218C>G	S1073C					6-33443770-C-G	1	6.23e-7	-8.862	Likely Pathogenic	0.461	Ambiguous	Likely Benign	0.137	Likely Benign										-1.52	Neutral	0.997	Probably Damaging	0.840	Possibly Damaging	3.81	Benign	0.00	Affected	3.77	5	-1	0	3.3	16.06
c.3221A>C	Q1074P					6-33443773-A-C	1	6.23e-7	-4.259	Likely Benign	0.083	Likely Benign	Likely Benign	0.188	Likely Benign										0.52	Neutral	0.925	Possibly Damaging	0.432	Benign	2.66	Benign	0.13	Tolerated	3.77	5	-1	0	1.9	-31.01
c.3221A>G	Q1074R					6-33443773-A-G			-5.710	Likely Benign	0.594	Likely Pathogenic	Likely Benign	0.124	Likely Benign										-0.54	Neutral	0.292	Benign	0.157	Benign	2.70	Benign	0.28	Tolerated	3.77	5	1	1	-1.0	28.06
c.3223C>A	Q1075K		Uncertain		1				-5.135	Likely Benign	0.728	Likely Pathogenic	Likely Benign	0.134	Likely Benign										-0.67	Neutral	0.963	Probably Damaging	0.959	Probably Damaging	2.75	Benign	1.00	Tolerated	3.77	5	1	1	-0.4	0.04
c.3229A>G	T1077A					6-33443781-A-G			-3.303	Likely Benign	0.280	Likely Benign	Likely Benign	0.153	Likely Benign										-0.60	Neutral	0.288	Benign	0.194	Benign	4.25	Benign	0.10	Tolerated	3.77	5	0	1	2.5	-30.03
c.3230C>T	T1077I					6-33443782-C-T	1	6.25e-7	-4.710	Likely Benign	0.919	Likely Pathogenic	Ambiguous	0.155	Likely Benign										-1.11	Neutral	0.970	Probably Damaging	0.787	Possibly Damaging	4.19	Benign	0.33	Tolerated	3.77	5	-1	0	5.2	12.05
c.3233T>A	V1078D		Uncertain		1				-5.155	Likely Benign	0.979	Likely Pathogenic	Likely Pathogenic	0.158	Likely Benign										-1.45	Neutral	0.003	Benign	0.008	Benign	3.84	Benign	0.00	Affected	3.77	5	-3	-2	-7.7	15.96
c.3235A>G	S1079G					6-33443787-A-G	6	3.76e-6	-3.552	Likely Benign	0.177	Likely Benign	Likely Benign	0.065	Likely Benign										-1.50	Neutral	0.036	Benign	0.018	Benign	3.87	Benign	0.00	Affected	3.77	5	0	1	0.4	-30.03
c.3237C>A	S1079R					6-33443789-C-A	4	2.51e-6	-4.579	Likely Benign	0.955	Likely Pathogenic	Ambiguous	0.123	Likely Benign										-1.81	Neutral	0.177	Benign	0.075	Benign	3.86	Benign	0.00	Affected	3.77	5	0	-1	-3.7	69.11
c.3237C>G	S1079R		Benign		1				-4.579	Likely Benign	0.955	Likely Pathogenic	Ambiguous	0.124	Likely Benign										-1.81	Neutral	0.177	Benign	0.075	Benign	3.86	Benign	0.00	Affected	3.77	5	0	-1	-3.7	69.11
c.3238G>A	A1080T		Conflicting		2	6-33443790-G-A	17	1.06e-5	-3.928	Likely Benign	0.133	Likely Benign	Likely Benign	0.144	Likely Benign										-0.19	Neutral	0.253	Benign	0.042	Benign	4.10	Benign	0.60	Tolerated	3.77	5	1	0	-2.5	30.03
c.3238G>T	A1080S		Uncertain		1	6-33443790-G-T	1	6.26e-7	-3.277	Likely Benign	0.108	Likely Benign	Likely Benign	0.103	Likely Benign										0.01	Neutral	0.702	Possibly Damaging	0.346	Benign	4.16	Benign	0.08	Tolerated	3.77	5	1	1	-2.6	16.00
c.3239C>A	A1080E					6-33443791-C-A			-3.672	Likely Benign	0.855	Likely Pathogenic	Ambiguous	0.090	Likely Benign										-1.50	Neutral	0.901	Possibly Damaging	0.540	Possibly Damaging	4.00	Benign	0.01	Affected	3.77	5	-1	0	-5.3	58.04
c.3239C>T	A1080V					6-33443791-C-T			-4.087	Likely Benign	0.229	Likely Benign	Likely Benign	0.124	Likely Benign										-1.06	Neutral	0.481	Possibly Damaging	0.144	Benign	3.99	Benign	0.04	Affected	3.77	5	0	0	2.4	28.05
c.323A>G	K108R		Uncertain		1	6-33432188-A-G	6	3.72e-6	-2.892	Likely Benign	0.148	Likely Benign	Likely Benign	0.184	Likely Benign										0.37	Neutral	0.993	Probably Damaging	0.956	Probably Damaging	4.22	Benign	1.00	Tolerated	3.61	5	3	2	-0.6	28.01
c.3242C>T	A1081V					6-33443794-C-T			-3.973	Likely Benign	0.172	Likely Benign	Likely Benign	0.036	Likely Benign										-1.32	Neutral	0.611	Possibly Damaging	0.399	Benign	4.04	Benign	0.37	Tolerated	3.77	5	0	0	2.4	28.05
c.3244C>G	Q1082E					6-33443796-C-G			-3.437	Likely Benign	0.267	Likely Benign	Likely Benign	0.090	Likely Benign										-0.87	Neutral	0.112	Benign	0.026	Benign	4.19	Benign	0.07	Tolerated	3.77	5	2	2	0.0	0.98
c.3246G>T	Q1082H					6-33443798-G-T			-4.307	Likely Benign	0.273	Likely Benign	Likely Benign	0.092	Likely Benign										-1.27	Neutral	0.002	Benign	0.002	Benign	4.11	Benign	0.03	Affected	3.77	5	0	3	0.3	9.01
c.3248A>C	K1083T					6-33443800-A-C	2	1.26e-6	-2.870	Likely Benign	0.690	Likely Pathogenic	Likely Benign	0.233	Likely Benign										-0.76	Neutral	0.999	Probably Damaging	0.995	Probably Damaging	4.05	Benign	0.31	Tolerated	3.77	5	-1	0	3.2	-27.07
c.324G>C	K108N					6-33432189-G-C	1	6.20e-7	-3.015	Likely Benign	0.964	Likely Pathogenic	Likely Pathogenic	0.068	Likely Benign										-1.35	Neutral	0.998	Probably Damaging	0.981	Probably Damaging	4.07	Benign	0.03	Affected	3.61	5	0	1	0.4	-14.07
c.3250C>A	P1084T					6-33443802-C-A			-4.665	Likely Benign	0.089	Likely Benign	Likely Benign	0.127	Likely Benign										-2.14	Neutral	0.025	Benign	0.012	Benign	4.11	Benign	0.01	Affected	3.77	5	-1	0	0.9	3.99
c.3250C>G	P1084A		Uncertain		1				-3.928	Likely Benign	0.066	Likely Benign	Likely Benign	0.114	Likely Benign										-2.54	Deleterious	0.649	Possibly Damaging	0.157	Benign	4.05	Benign	0.35	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3250C>T	P1084S					6-33443802-C-T	1	6.31e-7	-3.987	Likely Benign	0.119	Likely Benign	Likely Benign	0.086	Likely Benign										-2.24	Neutral	0.481	Possibly Damaging	0.157	Benign	4.03	Benign	0.03	Affected	3.77	5	-1	1	0.8	-10.04
c.3251C>A	P1084H		Uncertain		1	6-33443803-C-A	1	6.31e-7	-4.125	Likely Benign	0.323	Likely Benign	Likely Benign	0.134	Likely Benign										-3.16	Deleterious	0.997	Probably Damaging	0.840	Possibly Damaging	3.96	Benign	0.00	Affected	3.77	5	-2	0	-1.6	40.02
c.3251C>G	P1084R					6-33443803-C-G	4	2.52e-6	-4.171	Likely Benign	0.561	Ambiguous	Likely Benign	0.153	Likely Benign										-2.87	Deleterious	0.970	Probably Damaging	0.637	Possibly Damaging	3.99	Benign	0.01	Affected	3.77	5	-2	0	-2.9	59.07
c.3251C>T	P1084L					6-33443803-C-T	1	6.31e-7	-4.547	Likely Benign	0.175	Likely Benign	Likely Benign	0.124	Likely Benign										-3.33	Deleterious	0.649	Possibly Damaging	0.157	Benign	4.00	Benign	0.01	Affected	3.77	5	-3	-3	5.4	16.04
c.3253C>G	R1085G					6-33443805-C-G			-4.225	Likely Benign	0.846	Likely Pathogenic	Ambiguous	0.179	Likely Benign										-2.79	Deleterious	0.997	Probably Damaging	0.993	Probably Damaging	2.72	Benign	0.01	Affected	3.77	5	-2	-3	4.1	-99.14
c.3253C>T	R1085W					6-33443805-C-T	2	1.26e-6	-6.339	Likely Benign	0.821	Likely Pathogenic	Ambiguous	0.202	Likely Benign										-3.15	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	2.70	Benign	0.00	Affected	3.77	5	-3	2	3.6	30.03
c.3254G>A	R1085Q		Uncertain		1	6-33443806-G-A	5	3.16e-6	-3.843	Likely Benign	0.589	Likely Pathogenic	Likely Benign	0.224	Likely Benign										-1.43	Neutral	0.998	Probably Damaging	0.988	Probably Damaging	2.73	Benign	0.02	Affected	3.77	5	1	1	1.0	-28.06
c.3256C>A	P1086T					6-33443808-C-A			-4.181	Likely Benign	0.568	Likely Pathogenic	Likely Benign	0.229	Likely Benign										-2.97	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.75	Benign	0.00	Affected	3.77	5	-1	0	0.9	3.99
c.3256C>T	P1086S					6-33443808-C-T			-3.165	Likely Benign	0.604	Likely Pathogenic	Likely Benign	0.212	Likely Benign										-3.04	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.78	Benign	0.00	Affected	3.77	5	-1	1	0.8	-10.04
c.3257C>A	P1086Q					6-33443809-C-A			-4.668	Likely Benign	0.652	Likely Pathogenic	Likely Benign	0.185	Likely Benign										-2.92	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.77	Benign	0.00	Affected	3.77	5	-1	0	-1.9	31.01
c.3259T>C	S1087P					6-33443811-T-C	1	6.34e-7	-2.946	Likely Benign	0.133	Likely Benign	Likely Benign	0.135	Likely Benign										-1.92	Neutral	0.006	Benign	0.008	Benign	2.56	Benign	0.12	Tolerated	3.77	5	-1	1	-0.8	10.04
c.3260C>A	S1087Y					6-33443812-C-A			-4.194	Likely Benign	0.587	Likely Pathogenic	Likely Benign	0.107	Likely Benign										-2.41	Neutral	0.990	Probably Damaging	0.796	Possibly Damaging	2.56	Benign	0.02	Affected	3.77	5	-2	-3	-0.5	76.10
c.3260C>G	S1087C					6-33443812-C-G	1	6.34e-7	-7.369	In-Between	0.194	Likely Benign	Likely Benign	0.083	Likely Benign										-2.22	Neutral	0.997	Probably Damaging	0.840	Possibly Damaging	2.55	Benign	0.05	Affected	3.77	5	-1	0	3.3	16.06
c.3260C>T	S1087F		Uncertain		1				-3.843	Likely Benign	0.497	Ambiguous	Likely Benign	0.105	Likely Benign										-2.75	Deleterious	0.990	Probably Damaging	0.796	Possibly Damaging	2.56	Benign	0.03	Affected	3.77	5	-2	-3	3.6	60.10
c.3262A>G	S1088G		Uncertain		1				-5.034	Likely Benign	0.285	Likely Benign	Likely Benign	0.163	Likely Benign										-1.83	Neutral	0.979	Probably Damaging	0.973	Probably Damaging	2.63	Benign	0.03	Affected	3.77	5	0	1	0.4	-30.03
c.3263G>T	S1088I					6-33443815-G-T			-4.893	Likely Benign	0.891	Likely Pathogenic	Ambiguous	0.288	Likely Benign										-2.05	Neutral	0.997	Probably Damaging	0.995	Probably Damaging	2.62	Benign	0.01	Affected	3.77	5	-2	-1	5.3	26.08
c.3264C>A	S1088R					6-33443816-C-A			-4.588	Likely Benign	0.988	Likely Pathogenic	Likely Pathogenic	0.181	Likely Benign										-1.96	Neutral	0.999	Probably Damaging	0.996	Probably Damaging	2.72	Benign	0.01	Affected	3.77	5	-1	0	-3.7	69.11
c.3265G>A	G1089R					6-33443817-G-A	1	6.35e-7	-4.757	Likely Benign	0.897	Likely Pathogenic	Ambiguous	0.222	Likely Benign										-3.13	Deleterious	0.896	Possibly Damaging	0.325	Benign	2.42	Pathogenic	0.01	Affected	3.77	5	-2	-3	-4.1	99.14
c.326G>C	S109T					6-33432191-G-C	2	1.24e-6	-4.065	Likely Benign	0.449	Ambiguous	Likely Benign	0.090	Likely Benign										-1.19	Neutral	0.231	Benign	0.050	Benign	3.59	Benign	0.00	Affected	3.61	5	1	1	0.1	14.03
c.3270T>A	N1090K					6-33443822-T-A	2	1.28e-6	-3.423	Likely Benign	0.963	Likely Pathogenic	Likely Pathogenic	0.053	Likely Benign										-1.52	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.73	Benign	0.18	Tolerated	3.77	5	0	1	-0.4	14.07
c.3271C>A	L1091I					6-33443823-C-A			-4.304	Likely Benign	0.273	Likely Benign	Likely Benign	0.057	Likely Benign										-0.66	Neutral	0.186	Benign	0.055	Benign	2.55	Benign	0.13	Tolerated	3.77	5	2	2	0.7	0.00
c.3272T>C	L1091P					6-33443824-T-C			-4.139	Likely Benign	0.871	Likely Pathogenic	Ambiguous	0.180	Likely Benign										-1.25	Neutral	0.997	Probably Damaging	0.939	Probably Damaging	2.45	Pathogenic	0.04	Affected	3.77	5	-3	-3	-5.4	-16.04
c.3276G>C	L1092F					6-33443828-G-C	1	6.40e-7	-5.010	Likely Benign	0.623	Likely Pathogenic	Likely Benign	0.067	Likely Benign										-1.40	Neutral	0.986	Probably Damaging	0.823	Possibly Damaging	2.63	Benign	0.18	Tolerated	3.77	5	0	2	-1.0	34.02
c.3277C>A	Q1093K					6-33443829-C-A			-3.919	Likely Benign	0.558	Ambiguous	Likely Benign	0.061	Likely Benign										-0.92	Neutral	0.224	Benign	0.091	Benign	2.78	Benign	0.06	Tolerated	3.77	5	1	1	-0.4	0.04
c.3278A>G	Q1093R					6-33443830-A-G	1	6.40e-7	-3.681	Likely Benign	0.482	Ambiguous	Likely Benign	0.065	Likely Benign										-1.06	Neutral	0.224	Benign	0.091	Benign	2.73	Benign	0.04	Affected	3.77	5	1	1	-1.0	28.06
c.3281C>A	S1094Y					6-33443833-C-A			-5.609	Likely Benign	0.631	Likely Pathogenic	Likely Benign	0.155	Likely Benign										-2.07	Neutral	0.990	Probably Damaging	0.856	Possibly Damaging	2.45	Pathogenic	0.02	Affected	3.77	5	-2	-3	-0.5	76.10
c.3283C>T	P1095S					6-33443835-C-T	7	4.51e-6	-3.819	Likely Benign	0.182	Likely Benign	Likely Benign	0.128	Likely Benign										-0.64	Neutral	0.207	Benign	0.072	Benign	2.80	Benign	1.00	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3284C>T	P1095L					6-33443836-C-T	1	6.44e-7	-4.697	Likely Benign	0.363	Ambiguous	Likely Benign	0.126	Likely Benign										-2.78	Deleterious	0.960	Probably Damaging	0.604	Possibly Damaging	2.74	Benign	0.03	Affected	3.77	5	-3	-3	5.4	16.04
c.3287A>C	E1096A		Uncertain		1				-4.504	Likely Benign	0.510	Ambiguous	Likely Benign	0.164	Likely Benign										-1.37	Neutral	0.626	Possibly Damaging	0.184	Benign	2.77	Benign	0.16	Tolerated	3.77	5	-1	0	5.3	-58.04
c.3290C>A	P1097Q					6-33443842-C-A			-4.765	Likely Benign	0.198	Likely Benign	Likely Benign	0.092	Likely Benign										-1.10	Neutral	0.918	Possibly Damaging	0.604	Possibly Damaging	2.58	Benign	0.12	Tolerated	3.77	5	-1	0	-1.9	31.01
c.3290C>T	P1097L		Benign		1				-4.410	Likely Benign	0.145	Likely Benign	Likely Benign	0.131	Likely Benign										-2.07	Neutral	0.611	Possibly Damaging	0.198	Benign	2.64	Benign	0.05	Affected	3.77	5	-3	-3	5.4	16.04
c.3293G>A	S1098N		Conflicting		2	6-33443845-G-A	6	3.89e-6	-5.120	Likely Benign	0.156	Likely Benign	Likely Benign	0.063	Likely Benign										-0.58	Neutral	0.369	Benign	0.120	Benign	2.76	Benign	0.36	Tolerated	3.77	5	1	1	-2.7	27.03
c.3293G>T	S1098I					6-33443845-G-T			-4.497	Likely Benign	0.182	Likely Benign	Likely Benign	0.139	Likely Benign										-0.92	Neutral	0.259	Benign	0.066	Benign	2.67	Benign	0.15	Tolerated	3.77	5	-2	-1	5.3	26.08
c.3295T>C	Y1099H					6-33443847-T-C	1	6.49e-7	-3.620	Likely Benign	0.267	Likely Benign	Likely Benign	0.123	Likely Benign										-0.50	Neutral	0.990	Probably Damaging	0.796	Possibly Damaging	2.76	Benign	0.18	Tolerated	3.77	5	2	0	-1.9	-26.03
c.3296A>G	Y1099C					6-33443848-A-G	3	1.95e-6	-5.670	Likely Benign	0.109	Likely Benign	Likely Benign	0.122	Likely Benign										-1.13	Neutral	0.997	Probably Damaging	0.840	Possibly Damaging	2.73	Benign	0.14	Tolerated	3.77	5	-2	0	3.8	-60.04
c.3299G>T	G1100V					6-33443851-G-T	1	6.51e-7	-2.362	Likely Benign	0.118	Likely Benign	Likely Benign	0.198	Likely Benign										-2.43	Neutral	0.992	Probably Damaging	0.906	Possibly Damaging	1.93	Pathogenic	0.01	Affected	3.77	5	-3	-1	4.6	42.08
c.32G>A	G11E					6-33420296-G-A	5	3.24e-6	-4.206	Likely Benign	0.219	Likely Benign	Likely Benign	0.109	Likely Benign										0.09	Neutral	0.000	Benign	0.000	Benign	3.95	Benign	0.00	Affected	4.32	1	-2	0	-3.1	72.06
c.32G>T	G11V					6-33420296-G-T			-4.079	Likely Benign	0.160	Likely Benign	Likely Benign	0.146	Likely Benign										-0.38	Neutral	0.668	Possibly Damaging	0.049	Benign	3.93	Benign	0.00	Affected	4.32	1	-3	-1	4.6	42.08
c.3301C>T	P1101S					6-33443853-C-T	1	6.52e-7	-3.845	Likely Benign	0.080	Likely Benign	Likely Benign	0.075	Likely Benign										-1.31	Neutral	0.626	Possibly Damaging	0.255	Benign	4.25	Benign	0.07	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3304G>A	A1102T		Uncertain		1	6-33443856-G-A	11	7.17e-6	-3.540	Likely Benign	0.070	Likely Benign	Likely Benign	0.044	Likely Benign										-0.30	Neutral	0.001	Benign	0.001	Benign	2.32	Pathogenic	0.95	Tolerated	3.77	5	1	0	-2.5	30.03
c.3304G>C	A1102P		Uncertain		1				-5.120	Likely Benign	0.077	Likely Benign	Likely Benign	0.118	Likely Benign										-0.97	Neutral	0.000	Benign	0.002	Benign	2.26	Pathogenic	0.13	Tolerated	3.77	5	-1	1	-3.4	26.04
c.3305C>T	A1102V		Benign		1	6-33443857-C-T			-2.440	Likely Benign	0.077	Likely Benign	Likely Benign	0.081	Likely Benign										-1.27	Neutral	0.017	Benign	0.028	Benign	2.29	Pathogenic	0.12	Tolerated	3.77	5	0	0	2.4	28.05
c.3307C>T	R1103C		Uncertain		1	6-33443859-C-T	6	3.92e-6	-2.440	Likely Benign	0.246	Likely Benign	Likely Benign	0.140	Likely Benign										-3.01	Deleterious	0.996	Probably Damaging	0.787	Possibly Damaging	2.41	Pathogenic	0.01	Affected	3.77	5	-3	-4	7.0	-53.05
c.3308G>A	R1103H		Benign/Likely benign		3	6-33443860-G-A	31	2.03e-5	-3.622	Likely Benign	0.156	Likely Benign	Likely Benign	0.116	Likely Benign										-1.97	Neutral	0.996	Probably Damaging	0.733	Possibly Damaging	2.49	Pathogenic	0.01	Affected	3.77	5	2	0	1.3	-19.05
c.3308G>T	R1103L		Uncertain		1	6-33443860-G-T			-2.330	Likely Benign	0.205	Likely Benign	Likely Benign	0.173	Likely Benign										-2.35	Neutral	0.002	Benign	0.005	Benign	2.44	Pathogenic	0.02	Affected	3.77	5	-3	-2	8.3	-43.03
c.3310C>A	P1104T					6-33443862-C-A			-3.995	Likely Benign	0.070	Likely Benign	Likely Benign	0.094	Likely Benign										-0.14	Neutral	0.770	Possibly Damaging	0.481	Possibly Damaging	2.76	Benign	0.09	Tolerated	3.77	5	-1	0	0.9	3.99
c.3310C>T	P1104S		Benign		1	6-33443862-C-T	1	6.54e-7	-2.330	Likely Benign	0.073	Likely Benign	Likely Benign	0.088	Likely Benign										-0.30	Neutral	0.770	Possibly Damaging	0.404	Benign	2.77	Benign	0.10	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3311C>A	P1104Q					6-33443863-C-A			-3.161	Likely Benign	0.104	Likely Benign	Likely Benign	0.114	Likely Benign										-0.64	Neutral	0.986	Probably Damaging	0.825	Possibly Damaging	2.68	Benign	0.06	Tolerated	3.77	5	-1	0	-1.9	31.01
c.3313C>T	R1105W					6-33443865-C-T	6	3.93e-6	-6.911	Likely Benign	0.487	Ambiguous	Likely Benign	0.133	Likely Benign										-4.34	Deleterious	0.999	Probably Damaging	0.696	Possibly Damaging	2.42	Pathogenic	0.02	Affected	3.77	5	-3	2	3.6	30.03
c.3314G>A	R1105Q		Uncertain		2	6-33443866-G-A	3	1.96e-6	-3.666	Likely Benign	0.216	Likely Benign	Likely Benign	0.104	Likely Benign										-1.21	Neutral	0.958	Probably Damaging	0.194	Benign	2.50	Benign	0.16	Tolerated	3.77	5	1	1	1.0	-28.06
c.3314G>T	R1105L					6-33443866-G-T			-4.031	Likely Benign	0.459	Ambiguous	Likely Benign	0.125	Likely Benign										-3.51	Deleterious	0.677	Possibly Damaging	0.168	Benign	2.46	Pathogenic	0.19	Tolerated	3.77	5	-2	-3	8.3	-43.03
c.3316C>A	Q1106K					6-33443868-C-A			-3.368	Likely Benign	0.527	Ambiguous	Likely Benign	0.115	Likely Benign										-2.49	Neutral	0.963	Probably Damaging	0.959	Probably Damaging	1.82	Pathogenic	0.16	Tolerated	3.77	5	1	1	-0.4	0.04
c.3323G>T	S1108I		Uncertain		1	6-33443875-G-T			-3.666	Likely Benign	0.292	Likely Benign	Likely Benign	0.145	Likely Benign										-3.73	Deleterious	0.971	Probably Damaging	0.604	Possibly Damaging	2.44	Pathogenic	0.10	Tolerated	3.77	5	-2	-1	5.3	26.08
c.3325C>G	L1109V					6-33443877-C-G			-5.490	Likely Benign	0.062	Likely Benign	Likely Benign	0.091	Likely Benign										-0.52	Neutral	0.001	Benign	0.005	Benign	2.72	Benign	0.19	Tolerated	4.32	2	1	2	0.4	-14.03
c.3326T>C	L1109P		Conflicting		2				-5.313	Likely Benign	0.120	Likely Benign	Likely Benign	0.151	Likely Benign										-0.52	Neutral	0.002	Benign	0.003	Benign	2.65	Benign	0.07	Tolerated	4.32	2	-3	-3	-5.4	-16.04
c.3328A>G	S1110G		Likely Benign		1				-4.674	Likely Benign	0.079	Likely Benign	Likely Benign	0.035	Likely Benign										-2.26	Neutral	0.036	Benign	0.026	Benign	2.19	Pathogenic	0.08	Tolerated	4.32	2	1	0	0.4	-30.03
c.3329G>T	S1110I					6-33443881-G-T			-6.124	Likely Benign	0.198	Likely Benign	Likely Benign	0.038	Likely Benign										-2.99	Deleterious	0.007	Benign	0.003	Benign	2.17	Pathogenic	0.01	Affected	4.32	2	-2	-1	5.3	26.08
c.3332A>C	K1111T					6-33443884-A-C	2	1.32e-6	-4.037	Likely Benign	0.519	Ambiguous	Likely Benign	0.080	Likely Benign										-0.90	Neutral	0.292	Benign	0.110	Benign	2.64	Benign	0.28	Tolerated	4.32	2	-1	0	3.2	-27.07
c.3335A>G	E1112G					6-33443887-A-G	1	6.73e-7	-3.459	Likely Benign	0.277	Likely Benign	Likely Benign	0.124	Likely Benign										-2.58	Deleterious	0.058	Benign	0.015	Benign	2.70	Benign	0.01	Affected	4.32	2	-2	0	3.1	-72.06
c.3336G>T	E1112D					6-33443888-G-T			-4.286	Likely Benign	0.074	Likely Benign	Likely Benign	0.063	Likely Benign										-1.24	Neutral	0.005	Benign	0.005	Benign	2.69	Benign	0.06	Tolerated	4.32	2	2	3	0.0	-14.03
c.3338G>A	G1113D		Uncertain		1	6-33443890-G-A			-4.638	Likely Benign	0.354	Ambiguous	Likely Benign	0.061	Likely Benign										-0.72	Neutral	0.029	Benign	0.017	Benign	2.58	Benign	0.34	Tolerated	4.32	2	-1	1	-3.1	58.04
c.3340A>G	S1114G					6-33443892-A-G			-3.894	Likely Benign	0.064	Likely Benign	Likely Benign	0.080	Likely Benign										-1.33	Neutral	0.000	Benign	0.000	Benign	2.75	Benign	0.08	Tolerated	4.32	2	0	1	0.4	-30.03
c.3340A>T	S1114C					6-33443892-A-T			-8.600	Likely Pathogenic	0.091	Likely Benign	Likely Benign	0.038	Likely Benign										-1.77	Neutral	0.938	Possibly Damaging	0.552	Possibly Damaging	2.63	Benign	0.01	Affected	4.32	2	-1	0	3.3	16.06
c.3341G>T	S1114I					6-33443893-G-T			-6.718	Likely Benign	0.149	Likely Benign	Likely Benign	0.023	Likely Benign										-1.86	Neutral	0.570	Possibly Damaging	0.292	Benign	2.65	Benign	0.02	Affected	4.32	2	-2	-1	5.3	26.08
c.3343A>C	I1115L					6-33443895-A-C	1	7.56e-7	-2.308	Likely Benign	0.067	Likely Benign	Likely Benign	0.120	Likely Benign										-0.46	Neutral	0.004	Benign	0.007	Benign	2.82	Benign	1.00	Tolerated	4.32	2	2	2	-0.7	0.00
c.3343A>T	I1115F					6-33443895-A-T			-3.426	Likely Benign	0.095	Likely Benign	Likely Benign	0.097	Likely Benign										-0.98	Neutral	0.230	Benign	0.098	Benign	2.71	Benign	0.19	Tolerated	4.32	2	0	1	-1.7	34.02
c.3344T>C	I1115T		Benign		9	6-33443896-T-C	20536	1.36e-2	-2.670	Likely Benign	0.068	Likely Benign	Likely Benign	0.100	Likely Benign										-0.04	Neutral	0.000	Benign	0.001	Benign	2.76	Benign	0.23	Tolerated	4.32	2	0	-1	-5.2	-12.05
c.3344T>G	I1115S					6-33443896-T-G			-0.579	Likely Benign	0.073	Likely Benign	Likely Benign	0.128	Likely Benign										0.67	Neutral	0.000	Benign	0.001	Benign	2.88	Benign	0.14	Tolerated	4.32	2	-2	-1	-5.3	-26.08
c.3345T>G	I1115M					6-33443897-T-G	4	2.77e-6	-3.708	Likely Benign	0.067	Likely Benign	Likely Benign	0.106	Likely Benign										-0.38	Neutral	0.512	Possibly Damaging	0.200	Benign	2.71	Benign	0.23	Tolerated	4.32	2	1	2	-2.6	18.03
c.3346G>T	G1116W					6-33443898-G-T			-9.448	Likely Pathogenic	0.356	Ambiguous	Likely Benign	0.405	Likely Benign										-1.27	Neutral	0.996	Probably Damaging	0.946	Probably Damaging	4.04	Benign	0.01	Affected	4.32	2	-2	-7	-0.5	129.16
c.3347G>A	G1116E					6-33443899-G-A			-6.375	Likely Benign	0.375	Ambiguous	Likely Benign	0.345	Likely Benign										-0.33	Neutral	0.043	Benign	0.022	Benign	4.06	Benign	0.07	Tolerated	4.32	2	-2	0	-3.1	72.06
c.3347G>T	G1116V					6-33443899-G-T			-6.426	Likely Benign	0.102	Likely Benign	Likely Benign	0.393	Likely Benign										-0.79	Neutral	0.626	Possibly Damaging	0.375	Benign	4.06	Benign	0.06	Tolerated	4.32	2	-3	-1	4.6	42.08
c.3350G>A	G1117D					6-33443902-G-A	1	6.61e-7	-7.594	In-Between	0.357	Ambiguous	Likely Benign	0.315	Likely Benign										-0.38	Neutral	0.666	Possibly Damaging	0.355	Benign	4.57	Benign	0.24	Tolerated	4.32	2	-1	1	-3.1	58.04
c.3352A>G	S1118G					6-33443904-A-G	1	6.98e-7	-1.615	Likely Benign	0.057	Likely Benign	Likely Benign	0.146	Likely Benign										-0.61	Neutral	0.790	Possibly Damaging	0.433	Benign	5.82	Benign	0.08	Tolerated	4.32	2	0	1	0.4	-30.03
c.3352A>T	S1118C					6-33443904-A-T			-7.402	In-Between	0.096	Likely Benign	Likely Benign	0.311	Likely Benign										-1.05	Neutral	0.997	Probably Damaging	0.889	Possibly Damaging	5.15	Benign	0.01	Affected	4.32	2	-1	0	3.3	16.06
c.3354C>A	S1118R		Uncertain		1				-2.670	Likely Benign	0.553	Ambiguous	Likely Benign	0.166	Likely Benign										-0.74	Neutral	0.034	Benign	0.023	Benign	5.17	Benign	0.05	Affected	4.32	2	-1	0	-3.7	69.11
c.3354C>G	S1118R					6-33443906-C-G			-2.670	Likely Benign	0.553	Ambiguous	Likely Benign	0.165	Likely Benign										-0.74	Neutral	0.034	Benign	0.023	Benign	5.17	Benign	0.05	Affected	4.32	2	-1	0	-3.7	69.11
c.3355G>A	G1119R		Benign		1	6-33443907-G-A	64	4.23e-5	-8.489	Likely Pathogenic	0.473	Ambiguous	Likely Benign	0.303	Likely Benign										0.10	Neutral	0.969	Probably Damaging	0.462	Possibly Damaging	4.03	Benign	0.10	Tolerated	4.32	2	-3	-2	-4.1	99.14
c.3355G>T	G1119W					6-33443907-G-T			-10.904	Likely Pathogenic	0.336	Likely Benign	Likely Benign	0.386	Likely Benign										-1.19	Neutral	0.997	Probably Damaging	0.949	Probably Damaging	3.90	Benign	0.02	Affected	4.32	2	-2	-7	-0.5	129.16
c.3356G>A	G1119E					6-33443908-G-A	1	6.61e-7	-9.151	Likely Pathogenic	0.338	Likely Benign	Likely Benign	0.284	Likely Benign										-0.41	Neutral	0.005	Benign	0.013	Benign	3.93	Benign	0.12	Tolerated	4.32	2	-2	0	-3.1	72.06
c.3359G>A	G1120D					6-33443911-G-A	4	2.65e-6	-9.244	Likely Pathogenic	0.378	Ambiguous	Likely Benign	0.351	Likely Benign										-0.82	Neutral	0.666	Possibly Damaging	0.355	Benign	3.60	Benign	0.19	Tolerated	3.77	5	-1	1	-3.1	58.04
c.3359G>T	G1120V					6-33443911-G-T			-7.659	In-Between	0.081	Likely Benign	Likely Benign	0.355	Likely Benign										-1.20	Neutral	0.292	Benign	0.157	Benign	3.61	Benign	0.06	Tolerated	3.77	5	-3	-1	4.6	42.08
c.335G>C	G112A		Uncertain		1	6-33432200-G-C	15	9.30e-6	-2.456	Likely Benign	0.119	Likely Benign	Likely Benign	0.114	Likely Benign										-2.34	Neutral	0.231	Benign	0.054	Benign	4.07	Benign	0.00	Affected	3.61	5	1	0	2.2	14.03
c.3361A>G	S1121G		Uncertain		1	6-33443913-A-G	1	7.00e-7	-1.220	Likely Benign	0.054	Likely Benign	Likely Benign	0.067	Likely Benign										-0.53	Neutral	0.003	Benign	0.004	Benign	6.63	Benign	0.00	Affected	3.77	5	0	1	0.4	-30.03
c.3361A>T	S1121C					6-33443913-A-T			-7.431	In-Between	0.094	Likely Benign	Likely Benign	0.354	Likely Benign										-0.99	Neutral	0.994	Probably Damaging	0.840	Possibly Damaging	5.43	Benign	0.00	Affected	3.77	5	-1	0	3.3	16.06
c.3363C>G	S1121R					6-33443915-C-G			-6.945	Likely Benign	0.597	Likely Pathogenic	Likely Benign	0.101	Likely Benign										-0.34	Neutral	0.016	Benign	0.015	Benign	5.45	Benign	0.00	Affected	3.77	5	-1	0	-3.7	69.11
c.3364G>A	G1122S		Benign/Likely benign		2	6-33443916-G-A	27	1.79e-5	-4.880	Likely Benign	0.071	Likely Benign	Likely Benign	0.189	Likely Benign										-0.08	Neutral	0.022	Benign	0.006	Benign	4.89	Benign	0.92	Tolerated	3.77	5	1	0	-0.4	30.03
c.3364G>T	G1122C					6-33443916-G-T			-8.895	Likely Pathogenic	0.110	Likely Benign	Likely Benign	0.375	Likely Benign										-1.30	Neutral	0.975	Probably Damaging	0.733	Possibly Damaging	4.48	Benign	0.08	Tolerated	3.77	5	-3	-3	2.9	46.09
c.3367G>A	G1123S					6-33443919-G-A			-4.918	Likely Benign	0.077	Likely Benign	Likely Benign	0.291	Likely Benign										-0.32	Neutral	0.292	Benign	0.157	Benign	4.66	Benign	0.57	Tolerated	3.77	5	0	1	-0.4	30.03
c.3367G>T	G1123C					6-33443919-G-T	1	6.64e-7	-9.329	Likely Pathogenic	0.118	Likely Benign	Likely Benign	0.353	Likely Benign										-1.17	Neutral	0.994	Probably Damaging	0.840	Possibly Damaging	4.34	Benign	0.10	Tolerated	3.77	5	-3	-3	2.9	46.09
c.3368G>A	G1123D		Uncertain		1	6-33443920-G-A	2	1.33e-6	-10.321	Likely Pathogenic	0.405	Ambiguous	Likely Benign	0.360	Likely Benign										-0.78	Neutral	0.500	Possibly Damaging	0.157	Benign	4.34	Benign	0.19	Tolerated	3.77	5	1	-1	-3.1	58.04
c.3370G>A	G1124R		Conflicting		3	6-33443922-G-A	24	1.60e-5	-8.918	Likely Pathogenic	0.534	Ambiguous	Likely Benign	0.243	Likely Benign										-0.58	Neutral	0.002	Benign	0.002	Benign	4.81	Benign	0.01	Affected	3.77	5	-3	-2	-4.1	99.14
c.3373G>A	G1125R					6-33443925-G-A			-8.463	Likely Pathogenic	0.542	Ambiguous	Likely Benign	0.291	Likely Benign										-0.54	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	4.56	Benign	0.04	Affected	3.77	5	-2	-3	-4.1	99.14
c.3373G>C	G1125R					6-33443925-G-C	1	6.68e-7	-8.463	Likely Pathogenic	0.542	Ambiguous	Likely Benign	0.290	Likely Benign										-0.54	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	4.56	Benign	0.04	Affected	3.77	5	-2	-3	-4.1	99.14
c.3374G>A	G1125E					6-33443926-G-A	11	7.34e-6	-9.849	Likely Pathogenic	0.353	Ambiguous	Likely Benign	0.264	Likely Benign										-0.32	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	4.58	Benign	0.09	Tolerated	3.77	5	-2	0	-3.1	72.06
c.3374G>C	G1125A		Uncertain		1	6-33443926-G-C	1	6.68e-7	-6.569	Likely Benign	0.083	Likely Benign	Likely Benign	0.232	Likely Benign										-0.60	Neutral	0.999	Probably Damaging	0.995	Probably Damaging	4.60	Benign	0.11	Tolerated	3.77	5	1	0	2.2	14.03
c.3374G>T	G1125V					6-33443926-G-T			-6.776	Likely Benign	0.095	Likely Benign	Likely Benign	0.320	Likely Benign										-0.99	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	4.55	Benign	0.02	Affected	3.77	5	-3	-1	4.6	42.08
c.3376G>T	G1126C		Uncertain		1	6-33443928-G-T	11	7.35e-6	-9.389	Likely Pathogenic	0.113	Likely Benign	Likely Benign	0.449	Likely Benign										-1.40	Neutral	0.005	Benign	0.005	Benign	4.74	Benign	0.02	Affected	3.77	5	-3	-3	2.9	46.09
c.3377G>A	G1126D		Uncertain		1				-8.888	Likely Pathogenic	0.432	Ambiguous	Likely Benign	0.376	Likely Benign										-0.65	Neutral	0.906	Possibly Damaging	0.473	Possibly Damaging	4.82	Benign	0.02	Affected	3.77	5	1	-1	-3.1	58.04
c.3377G>T	G1126V		Uncertain		1	6-33443929-G-T			-6.536	Likely Benign	0.089	Likely Benign	Likely Benign	0.357	Likely Benign										-1.20	Neutral	0.009	Benign	0.008	Benign	4.76	Benign	0.03	Affected	3.77	5	-1	-3	4.6	42.08
c.3379G>A	G1127R		Uncertain		1	6-33443931-G-A	2	1.34e-6	-5.949	Likely Benign	0.629	Likely Pathogenic	Likely Benign	0.341	Likely Benign										-0.87	Neutral	0.001	Benign	0.001	Benign	4.86	Benign	0.12	Tolerated	4.32	4	-2	-3	-4.1	99.14
c.3379G>C	G1127R		Uncertain		1	6-33443931-G-C	16	1.07e-5	-5.949	Likely Benign	0.629	Likely Pathogenic	Likely Benign	0.341	Likely Benign										-0.87	Neutral	0.001	Benign	0.001	Benign	4.86	Benign	0.12	Tolerated	4.32	4	-2	-3	-4.1	99.14
c.3379G>T	G1127W					6-33443931-G-T	3	2.01e-6	-9.850	Likely Pathogenic	0.417	Ambiguous	Likely Benign	0.394	Likely Benign										-1.36	Neutral	0.983	Probably Damaging	0.665	Possibly Damaging	4.79	Benign	0.03	Affected	4.32	4	-2	-7	-0.5	129.16
c.3380G>C	G1127A		Conflicting		4	6-33443932-G-C	4	2.68e-6	-5.949	Likely Benign	0.080	Likely Benign	Likely Benign	0.164	Likely Benign										-0.43	Neutral	0.001	Benign	0.002	Benign	4.83	Benign	1.00	Tolerated	4.32	4	1	0	2.2	14.03
c.3380G>T	G1127V		Uncertain		1	6-33443932-G-T	1	6.69e-7	-6.097	Likely Benign	0.093	Likely Benign	Likely Benign	0.230	Likely Benign										-1.01	Neutral	0.004	Benign	0.005	Benign	4.81	Benign	0.17	Tolerated	4.32	4	-1	-3	4.6	42.08
c.3383G>A	G1128E					6-33443935-G-A	1	6.70e-7	-5.580	Likely Benign	0.452	Ambiguous	Likely Benign	0.235	Likely Benign										-0.24	Neutral	0.002	Benign	0.008	Benign	4.43	Benign	1.00	Tolerated	4.32	4	-2	0	-3.1	72.06
c.3383G>T	G1128V					6-33443935-G-T			-5.111	Likely Benign	0.081	Likely Benign	Likely Benign	0.399	Likely Benign										-0.69	Neutral	0.611	Possibly Damaging	0.185	Benign	4.39	Benign	0.09	Tolerated	4.32	4	-3	-1	4.6	42.08
c.3386T>C	L1129P		Uncertain		2				-2.991	Likely Benign	0.154	Likely Benign	Likely Benign	0.432	Likely Benign										0.27	Neutral	0.971	Probably Damaging	0.773	Possibly Damaging	5.44	Benign	0.00	Affected	4.32	4	-3	-3	-5.4	-16.04
c.3388A>C	K1130Q					6-33443940-A-C			-3.548	Likely Benign	0.529	Ambiguous	Likely Benign	0.337	Likely Benign										-1.25	Neutral	0.818	Possibly Damaging	0.355	Benign	5.44	Benign	0.00	Affected	4.32	4	1	1	0.4	-0.04
c.3389A>G	K1130R					6-33443941-A-G			-2.163	Likely Benign	0.155	Likely Benign	Likely Benign	0.187	Likely Benign										-0.94	Neutral	0.014	Benign	0.008	Benign	5.44	Benign	0.00	Affected	4.32	4	2	3	-0.6	28.01
c.338G>A	G113E					6-33432203-G-A	1	6.20e-7	-3.169	Likely Benign	0.669	Likely Pathogenic	Likely Benign	0.092	Likely Benign										-0.34	Neutral	0.028	Benign	0.006	Benign	4.21	Benign	0.05	Affected	3.61	5	-2	0	-3.1	72.06
c.3391C>T	P1131S					6-33443943-C-T	1	6.72e-7	-4.089	Likely Benign	0.246	Likely Benign	Likely Benign	0.209	Likely Benign										-2.62	Deleterious	0.025	Benign	0.015	Benign	5.54	Benign	0.00	Affected	4.32	4	-1	1	0.8	-10.04
c.3394T>C	S1132P		Uncertain		2	6-33443946-T-C	1	6.74e-7	-1.423	Likely Benign	0.144	Likely Benign	Likely Benign	0.301	Likely Benign										0.38	Neutral	0.003	Benign	0.006	Benign	5.40	Benign	0.28	Tolerated	4.32	4	1	-1	-0.8	10.04
c.3395C>A	S1132Y		Likely Benign		1				-5.894	Likely Benign	0.392	Ambiguous	Likely Benign	0.401	Likely Benign										-1.76	Neutral	0.500	Possibly Damaging	0.208	Benign	5.40	Benign	0.09	Tolerated	4.32	4	-3	-2	-0.5	76.10
c.3397A>G	I1133V		Benign		1	6-33443949-A-G	22	1.48e-5	-3.362	Likely Benign	0.067	Likely Benign	Likely Benign	0.180	Likely Benign										0.06	Neutral	0.007	Benign	0.007	Benign	5.47	Benign	0.58	Tolerated	4.32	3	4	3	-0.3	-14.03																10.1016/j.ajhg.2020.11.011
c.3398T>C	I1133T					6-33443950-T-C			-4.522	Likely Benign	0.563	Ambiguous	Likely Benign	0.275	Likely Benign										-0.30	Neutral	0.026	Benign	0.030	Benign	5.50	Benign	0.18	Tolerated	4.32	3	-1	0	-5.2	-12.05
c.3403A>G	K1135E					6-33443955-A-G			-6.499	Likely Benign	0.924	Likely Pathogenic	Ambiguous	0.239	Likely Benign										-0.76	Neutral	0.224	Benign	0.237	Benign	5.45	Benign	0.12	Tolerated	4.32	2	1	0	0.4	0.94
c.3404A>C	K1135T		Conflicting		2	6-33443956-A-C	1	6.75e-7	-4.778	Likely Benign	0.779	Likely Pathogenic	Likely Benign	0.210	Likely Benign										-0.90	Neutral	0.411	Benign	0.321	Benign	5.46	Benign	0.10	Tolerated	4.32	2	0	-1	3.2	-27.07
c.3405G>C	K1135N		Uncertain		1				-5.715	Likely Benign	0.960	Likely Pathogenic	Likely Pathogenic	0.166	Likely Benign										-0.97	Neutral	0.411	Benign	0.321	Benign	5.43	Benign	0.07	Tolerated	4.32	2	1	0	0.4	-14.07
c.3405G>T	K1135N					6-33443957-G-T			-5.715	Likely Benign	0.960	Likely Pathogenic	Likely Pathogenic	0.166	Likely Benign										-0.97	Neutral	0.411	Benign	0.321	Benign	5.43	Benign	0.07	Tolerated	4.32	2	1	0	0.4	-14.07
c.3406C>A	Q1136K					6-33443958-C-A			-5.698	Likely Benign	0.397	Ambiguous	Likely Benign	0.236	Likely Benign										-1.43	Neutral	0.625	Possibly Damaging	0.258	Benign	5.55	Benign	0.17	Tolerated	4.32	2	1	1	-0.4	0.04
c.3406C>G	Q1136E					6-33443958-C-G	4	2.71e-6	-6.677	Likely Benign	0.277	Likely Benign	Likely Benign	0.209	Likely Benign										-1.13	Neutral	0.022	Benign	0.026	Benign	5.46	Benign	0.11	Tolerated	4.32	2	2	2	0.0	0.98
c.3408G>T	Q1136H					6-33443960-G-T			-5.658	Likely Benign	0.305	Likely Benign	Likely Benign	0.347	Likely Benign										-1.98	Neutral	0.989	Probably Damaging	0.879	Possibly Damaging	5.42	Benign	0.03	Affected	4.32	2	0	3	0.3	9.01
c.3410A>C	H1137P					6-33444445-A-C	12	7.44e-6	-2.098	Likely Benign	0.054	Likely Benign	Likely Benign	0.419	Likely Benign										-1.93	Neutral	0.925	Possibly Damaging	0.703	Possibly Damaging	5.29	Benign	0.00	Affected	4.32	4	-2	0	1.6	-40.02
c.3410A>G	H1137R					6-33444445-A-G	1	6.20e-7	-3.468	Likely Benign	0.228	Likely Benign	Likely Benign	0.296	Likely Benign										-1.19	Neutral	0.925	Possibly Damaging	0.629	Possibly Damaging	5.32	Benign	0.00	Affected	4.32	4	0	2	-1.3	19.05
c.3413C>A	S1138Y					6-33444448-C-A	3	1.86e-6	-6.610	Likely Benign	0.449	Ambiguous	Likely Benign	0.391	Likely Benign										-2.51	Deleterious	0.997	Probably Damaging	0.996	Probably Damaging	5.41	Benign	0.05	Affected	4.32	4	-2	-3	-0.5	76.10
c.3413C>G	S1138C					6-33444448-C-G	1	6.20e-7	-7.850	In-Between	0.117	Likely Benign	Likely Benign	0.425	Likely Benign										-2.48	Neutral	0.999	Probably Damaging	0.997	Probably Damaging	5.40	Benign	0.04	Affected	4.32	4	-1	0	3.3	16.06
c.3413C>T	S1138F					6-33444448-C-T	1	6.20e-7	-6.298	Likely Benign	0.379	Ambiguous	Likely Benign	0.407	Likely Benign										-2.88	Deleterious	0.997	Probably Damaging	0.996	Probably Damaging	5.42	Benign	0.03	Affected	4.32	4	-2	-3	3.6	60.10
c.3419C>G	T1140R					6-33444454-C-G	1	6.20e-7	-4.245	Likely Benign	0.682	Likely Pathogenic	Likely Benign	0.073	Likely Benign										-1.69	Neutral	0.761	Possibly Damaging	0.398	Benign	2.61	Benign	0.15	Tolerated	4.32	4	-1	-1	-3.8	55.08
c.3424T>C	S1142P		Likely Benign		1	6-33444459-T-C	1	6.20e-7	-2.713	Likely Benign	0.222	Likely Benign	Likely Benign	0.107	Likely Benign										-2.19	Neutral	0.918	Possibly Damaging	0.761	Possibly Damaging	2.64	Benign	0.00	Affected	4.32	4	-1	1	-0.8	10.04
c.3431T>G	L1144W					6-33444466-T-G	1	6.20e-7	-5.745	Likely Benign	0.707	Likely Pathogenic	Likely Benign	0.575	Likely Pathogenic										-2.87	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	5.36	Benign	0.01	Affected	4.32	4	-2	-2	-4.7	73.05
c.3434A>C	N1145T					6-33444469-A-C	1	6.20e-7	-1.915	Likely Benign	0.217	Likely Benign	Likely Benign	0.403	Likely Benign										-2.17	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	5.45	Benign	0.07	Tolerated	4.32	4	0	0	2.8	-13.00
c.3434A>G	N1145S		Uncertain		1	6-33444469-A-G	2	1.24e-6	-0.989	Likely Benign	0.126	Likely Benign	Likely Benign	0.308	Likely Benign										-1.15	Neutral	0.997	Probably Damaging	0.989	Probably Damaging	5.55	Benign	0.89	Tolerated	4.32	4	1	1	2.7	-27.03
c.3436C>T	P1146S					6-33444471-C-T	2	1.24e-6	-3.045	Likely Benign	0.318	Likely Benign	Likely Benign	0.470	Likely Benign										-3.66	Deleterious	0.945	Possibly Damaging	0.760	Possibly Damaging	5.52	Benign	0.00	Affected	4.32	4	-1	1	0.8	-10.04
c.343C>G	Q115E					6-33432208-C-G	1	6.20e-7	-3.465	Likely Benign	0.229	Likely Benign	Likely Benign	0.096	Likely Benign										-0.40	Neutral	0.924	Possibly Damaging	0.857	Possibly Damaging	4.18	Benign	0.42	Tolerated	3.61	5	2	2	0.0	0.98
c.3442A>G	M1148V					6-33444477-A-G	3	1.86e-6	-2.358	Likely Benign	0.081	Likely Benign	Likely Benign	0.057	Likely Benign										-1.47	Neutral	0.016	Benign	0.026	Benign	2.59	Benign	0.00	Affected	4.32	2	1	2	2.3	-32.06
c.3442A>T	M1148L		Uncertain		1				-1.777	Likely Benign	0.093	Likely Benign	Likely Benign	0.068	Likely Benign										-1.13	Neutral	0.016	Benign	0.016	Benign	2.62	Benign	0.00	Affected	4.32	2	4	2	1.9	-18.03
c.3448G>T	A1150S					6-33444483-G-T	7	4.34e-6	-2.656	Likely Benign	0.126	Likely Benign	Likely Benign	0.122	Likely Benign										-1.49	Neutral	0.951	Possibly Damaging	0.752	Possibly Damaging	2.37	Pathogenic	0.10	Tolerated	3.77	5	1	1	-2.6	16.00
c.3449C>T	A1150V		Uncertain		1	6-33444484-C-T	3	1.86e-6	-3.648	Likely Benign	0.192	Likely Benign	Likely Benign	0.066	Likely Benign										-2.22	Neutral	0.114	Benign	0.055	Benign	2.32	Pathogenic	0.04	Affected	3.77	5	0	0	2.4	28.05
c.3452C>G	S1151C					6-33444487-C-G	1	6.20e-7	-6.778	Likely Benign	0.225	Likely Benign	Likely Benign	0.181	Likely Benign										-0.86	Neutral	0.999	Probably Damaging	0.944	Probably Damaging	2.67	Benign	0.07	Tolerated	3.77	5	-1	0	3.3	16.06
c.3454G>A	E1152K					6-33444489-G-A	1	6.20e-7	-3.612	Likely Benign	0.966	Likely Pathogenic	Likely Pathogenic	0.300	Likely Benign										-2.64	Deleterious	0.997	Probably Damaging	0.992	Probably Damaging	2.38	Pathogenic	0.02	Affected	3.77	5	1	0	-0.4	-0.94
c.3457C>T	R1153W		Uncertain		1	6-33444492-C-T	2	1.24e-6	-5.812	Likely Benign	0.994	Likely Pathogenic	Likely Pathogenic	0.317	Likely Benign										-5.88	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.46	Pathogenic	0.00	Affected	3.77	5	2	-3	3.6	30.03
c.3463G>A	V1155M					6-33444498-G-A	1	6.20e-7	-3.818	Likely Benign	0.915	Likely Pathogenic	Ambiguous	0.249	Likely Benign										-1.19	Neutral	0.999	Probably Damaging	0.998	Probably Damaging	2.57	Benign	0.02	Affected	3.77	5	1	2	-2.3	32.06
c.3466G>T	A1156S					6-33444501-G-T	1	6.20e-7	-2.052	Likely Benign	0.798	Likely Pathogenic	Ambiguous	0.197	Likely Benign										-2.23	Neutral	0.997	Probably Damaging	0.994	Probably Damaging	1.65	Pathogenic	0.00	Affected	3.77	5	1	1	-2.6	16.00
c.346T>C	Y116H					6-33432211-T-C	7	4.34e-6	-1.512	Likely Benign	0.378	Ambiguous	Likely Benign	0.080	Likely Benign										0.11	Neutral	0.539	Possibly Damaging	0.085	Benign	4.21	Benign	0.40	Tolerated	3.61	5	2	0	-1.9	-26.03
c.3481A>G	M1161V					6-33444516-A-G	2	1.24e-6	-3.060	Likely Benign	0.915	Likely Pathogenic	Ambiguous	0.150	Likely Benign										-1.85	Neutral	0.843	Possibly Damaging	0.926	Probably Damaging	2.27	Pathogenic	0.22	Tolerated	3.77	5	1	2	2.3	-32.06
c.3482T>C	M1161T					6-33444517-T-C	1	6.20e-7	-2.620	Likely Benign	0.997	Likely Pathogenic	Likely Pathogenic	0.148	Likely Benign										-2.75	Deleterious	0.968	Probably Damaging	0.954	Probably Damaging	2.19	Pathogenic	0.27	Tolerated	3.77	5	-1	-1	-2.6	-30.09
c.3483G>T	M1161I					6-33444518-G-T	1	6.20e-7	-3.124	Likely Benign	0.994	Likely Pathogenic	Likely Pathogenic	0.155	Likely Benign										-1.92	Neutral	0.925	Possibly Damaging	0.954	Probably Damaging	2.27	Pathogenic	0.25	Tolerated	3.77	5	1	2	2.6	-18.03
c.3484C>T	P1162S		Uncertain		1				-2.118	Likely Benign	0.913	Likely Pathogenic	Ambiguous	0.215	Likely Benign										-1.93	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	2.73	Benign	0.55	Tolerated	3.88	3	1	-1	0.8	-10.04
c.3487C>G	H1163D		Uncertain		1				-2.107	Likely Benign	0.949	Likely Pathogenic	Ambiguous	0.476	Likely Benign										-2.60	Deleterious	0.991	Probably Damaging	0.991	Probably Damaging	5.44	Benign	0.31	Tolerated	3.88	3	1	-1	-0.3	-22.05
c.3494C>T	S1165L		Conflicting		2				-2.984	Likely Benign	0.793	Likely Pathogenic	Ambiguous	0.166	Likely Benign										-2.01	Neutral	0.998	Probably Damaging	0.992	Probably Damaging	2.60	Benign	0.33	Tolerated	3.88	3	-3	-2	4.6	26.08																10.1016/j.ajhg.2020.11.011
c.34A>G	S12G					6-33420298-A-G			-4.229	Likely Benign	0.093	Likely Benign	Likely Benign	0.079	Likely Benign										0.22	Neutral	0.103	Benign	0.015	Benign	4.11	Benign	0.00	Affected	4.32	1	0	1	0.4	-30.03
c.3502A>G	I1168V		Uncertain		1				-3.263	Likely Benign	0.524	Ambiguous	Likely Benign	0.363	Likely Benign										-0.14	Neutral	0.876	Possibly Damaging	0.643	Possibly Damaging	5.47	Benign	0.84	Tolerated	3.88	3	4	3	-0.3	-14.03
c.3505G>A	E1169K					6-33444540-G-A	1	6.20e-7	-3.335	Likely Benign	0.973	Likely Pathogenic	Likely Pathogenic	0.185	Likely Benign										-1.81	Neutral	0.997	Probably Damaging	0.898	Possibly Damaging	2.51	Benign	0.00	Affected	3.88	3	1	0	-0.4	-0.94
c.3505G>C	E1169Q					6-33444540-G-C	1	6.20e-7	-3.096	Likely Benign	0.852	Likely Pathogenic	Ambiguous	0.119	Likely Benign										-1.27	Neutral	0.872	Possibly Damaging	0.701	Possibly Damaging	2.48	Pathogenic	0.00	Affected	3.88	3	2	2	0.0	-0.98
c.3508A>G	S1170G	Coiled-coil	Uncertain		1				-4.288	Likely Benign	0.221	Likely Benign	Likely Benign	0.349	Likely Benign										-0.81	Neutral	0.241	Benign	0.229	Benign	5.31	Benign	0.54	Tolerated	4.32	4	1	0	0.4	-30.03
c.3509G>A	S1170N	Coiled-coil				6-33444544-G-A	1	6.20e-7	-3.705	Likely Benign	0.412	Ambiguous	Likely Benign	0.342	Likely Benign										-0.18	Neutral	0.992	Probably Damaging	0.925	Probably Damaging	5.39	Benign	0.86	Tolerated	4.32	4	1	1	-2.7	27.03
c.3511G>A	A1171T	Coiled-coil	Uncertain		1				-3.658	Likely Benign	0.149	Likely Benign	Likely Benign	0.201	Likely Benign										-0.48	Neutral	0.245	Benign	0.138	Benign	5.45	Benign	0.07	Tolerated	4.32	4	1	0	-2.5	30.03
c.3511_3512delinsTG	A1171C	Coiled-coil	Uncertain		1				-5.363	Likely Benign	0.496	Ambiguous	Likely Benign												-1.16	Neutral	0.978	Probably Damaging	0.825	Possibly Damaging	5.32	Benign	0.02	Affected	4.32	4	-2	0	0.7	32.06
c.3517A>G	I1173V	Coiled-coil				6-33444552-A-G	1	6.20e-7	-3.564	Likely Benign	0.160	Likely Benign	Likely Benign	0.143	Likely Benign										-0.16	Neutral	0.011	Benign	0.006	Benign	5.55	Benign	0.36	Tolerated	4.32	4	3	4	-0.3	-14.03
c.351C>G	S117R					6-33432216-C-G	1	6.20e-7	-4.187	Likely Benign	0.971	Likely Pathogenic	Likely Pathogenic	0.144	Likely Benign										-1.81	Neutral	0.845	Possibly Damaging	0.326	Benign	3.70	Benign	0.01	Affected	3.61	5	-1	0	-3.7	69.11
c.3520G>A	E1174K	Coiled-coil	Uncertain		1	6-33444555-G-A	2	1.24e-6	-4.345	Likely Benign	0.898	Likely Pathogenic	Ambiguous	0.442	Likely Benign										-1.59	Neutral	0.962	Probably Damaging	0.367	Benign	5.52	Benign	0.03	Affected	4.32	2	0	1	-0.4	-0.94
c.3522G>C	E1174D	Coiled-coil				6-33444557-G-C	1	6.20e-7	-4.257	Likely Benign	0.253	Likely Benign	Likely Benign	0.234	Likely Benign										-0.19	Neutral	0.002	Benign	0.006	Benign	5.45	Benign	0.36	Tolerated	4.32	2	2	3	0.0	-14.03
c.3523C>T	R1175W	Coiled-coil				6-33444558-C-T	3	1.86e-6	-5.807	Likely Benign	0.907	Likely Pathogenic	Ambiguous	0.514	Likely Pathogenic										-2.83	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	5.32	Benign	0.00	Affected	4.32	2	-3	2	3.6	30.03
c.3524G>A	R1175Q	Coiled-coil				6-33444559-G-A	1	6.20e-7	-3.968	Likely Benign	0.529	Ambiguous	Likely Benign	0.328	Likely Benign										-0.76	Neutral	0.998	Probably Damaging	0.992	Probably Damaging	5.39	Benign	0.00	Affected	4.32	2	1	1	1.0	-28.06
c.3529G>A	E1177K	Coiled-coil	Uncertain		1				-3.413	Likely Benign	0.944	Likely Pathogenic	Ambiguous	0.560	Likely Pathogenic										-1.75	Neutral	0.905	Possibly Damaging	0.637	Possibly Damaging	5.44	Benign	0.11	Tolerated	4.32	2	0	1	-0.4	-0.94
c.3535A>C	K1179Q	Coiled-coil				6-33444570-A-C	1	6.20e-7	-4.237	Likely Benign	0.678	Likely Pathogenic	Likely Benign	0.078	Likely Benign										-1.20	Neutral	0.430	Benign	0.211	Benign	2.67	Benign	0.00	Affected	4.32	2	1	1	0.4	-0.04
c.3535A>G	K1179E	Coiled-coil				6-33444570-A-G	1	6.20e-7	-4.040	Likely Benign	0.961	Likely Pathogenic	Likely Pathogenic	0.143	Likely Benign										-1.02	Neutral	0.800	Possibly Damaging	0.525	Possibly Damaging	2.96	Benign	0.00	Affected	4.32	2	1	0	0.4	0.94
c.3541A>C	K1181Q	Coiled-coil				6-33444576-A-C			-3.724	Likely Benign	0.779	Likely Pathogenic	Likely Benign	0.173	Likely Benign										-1.48	Neutral	0.999	Probably Damaging	0.977	Probably Damaging	2.66	Benign	0.07	Tolerated	4.32	3	1	1	0.4	-0.04
c.3542A>G	K1181R	Coiled-coil				6-33444577-A-G	2	1.24e-6	-2.786	Likely Benign	0.185	Likely Benign	Likely Benign	0.088	Likely Benign										-0.90	Neutral	0.573	Possibly Damaging	0.429	Benign	2.67	Benign	0.07	Tolerated	4.32	3	2	3	-0.6	28.01
c.3554A>T	K1185I	Coiled-coil				6-33444589-A-T	1	6.20e-7	-5.101	Likely Benign	0.990	Likely Pathogenic	Likely Pathogenic	0.215	Likely Benign										-3.42	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	2.62	Benign	0.09	Tolerated	3.82	4	-3	-2	8.4	-15.01
c.3557C>T	S1186L	Coiled-coil	Uncertain		1	6-33444592-C-T			-4.829	Likely Benign	0.923	Likely Pathogenic	Ambiguous	0.177	Likely Benign										-2.58	Deleterious	0.998	Probably Damaging	0.992	Probably Damaging	2.65	Benign	0.04	Affected	3.82	4	-3	-2	4.6	26.08
c.3561G>A	M1187I	Coiled-coil				6-33444596-G-A	1	6.20e-7	-3.666	Likely Benign	0.993	Likely Pathogenic	Likely Pathogenic	0.366	Likely Benign										-1.65	Neutral	0.925	Possibly Damaging	0.954	Probably Damaging	5.46	Benign	0.32	Tolerated	3.82	4	1	2	2.6	-18.03
c.3567G>C	E1189D	Coiled-coil	Likely Benign		1	6-33444602-G-C	3	1.86e-6	-3.582	Likely Benign	0.461	Ambiguous	Likely Benign	0.359	Likely Benign										-1.42	Neutral	0.992	Probably Damaging	0.989	Probably Damaging	5.30	Benign	0.25	Tolerated	3.82	4	3	2	0.0	-14.03
c.3568A>G	S1190G	Coiled-coil				6-33444603-A-G	1	6.20e-7	-3.078	Likely Benign	0.647	Likely Pathogenic	Likely Benign	0.374	Likely Benign										-1.13	Neutral	0.979	Probably Damaging	0.982	Probably Damaging	5.28	Benign	0.42	Tolerated	3.82	4	0	1	0.4	-30.03
c.3569G>A	S1190N	Coiled-coil				6-33444604-G-A	2	1.24e-6	-4.909	Likely Benign	0.811	Likely Pathogenic	Ambiguous	0.326	Likely Benign										-1.25	Neutral	0.991	Probably Damaging	0.988	Probably Damaging	5.27	Benign	0.07	Tolerated	3.82	4	1	1	-2.7	27.03
c.3571C>T	R1191W	Coiled-coil				6-33444606-C-T	4	2.48e-6	-4.839	Likely Benign	0.987	Likely Pathogenic	Likely Pathogenic	0.320	Likely Benign										-3.16	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.61	Benign	0.01	Affected	3.82	4	-3	2	3.6	30.03
c.3572G>A	R1191Q	Coiled-coil	Uncertain		2	6-33444607-G-A	9	5.58e-6	-1.069	Likely Benign	0.943	Likely Pathogenic	Ambiguous	0.343	Likely Benign										-1.41	Neutral	0.998	Probably Damaging	0.992	Probably Damaging	2.68	Benign	0.08	Tolerated	3.82	4	1	1	1.0	-28.06
c.3578A>G	D1193G	Coiled-coil				6-33444613-A-G	1	6.21e-7	-6.506	Likely Benign	0.764	Likely Pathogenic	Likely Benign	0.480	Likely Benign										-2.27	Neutral	0.924	Possibly Damaging	0.652	Possibly Damaging	5.42	Benign	0.00	Affected	4.32	4	-1	1	3.1	-58.04
c.357G>T	E119D					6-33432222-G-T	3	1.86e-6	-3.258	Likely Benign	0.108	Likely Benign	Likely Benign	0.033	Likely Benign										0.07	Neutral	0.000	Benign	0.001	Benign	4.08	Benign	0.32	Tolerated	3.61	5	2	3	0.0	-14.03																10.1016/j.ajhg.2020.11.011
c.3581G>A	R1194K	Coiled-coil				6-33444616-G-A	1	6.21e-7	-2.501	Likely Benign	0.486	Ambiguous	Likely Benign	0.380	Likely Benign										-0.97	Neutral	0.979	Probably Damaging	0.982	Probably Damaging	5.56	Benign	0.14	Tolerated	3.77	5	2	3	0.6	-28.01
c.358G>A	G120S					6-33432223-G-A	1	6.20e-7	-3.558	Likely Benign	0.082	Likely Benign	Likely Benign	0.034	Likely Benign										0.07	Neutral	0.020	Benign	0.012	Benign	4.29	Benign	0.91	Tolerated	3.61	5	0	1	-0.4	30.03
c.3595G>A	E1199K	Coiled-coil	Uncertain		1	6-33446587-G-A	1	6.20e-7	-10.853	Likely Pathogenic	0.954	Likely Pathogenic	Ambiguous	0.171	Likely Benign										-2.26	Neutral	1.000	Probably Damaging	0.995	Probably Damaging	2.52	Benign	0.00	Affected	3.77	5	0	1	-0.4	-0.94
c.35G>A	S12N					6-33420299-G-A			-4.946	Likely Benign	0.185	Likely Benign	Likely Benign	0.069	Likely Benign										-0.41	Neutral	0.208	Benign	0.018	Benign	4.10	Benign	0.00	Affected	4.32	1	1	1	-2.7	27.03
c.3607C>G	H1203D	Coiled-coil	Uncertain		1				-6.729	Likely Benign	0.524	Ambiguous	Likely Benign	0.403	Likely Benign										-1.89	Neutral	0.473	Possibly Damaging	0.265	Benign	5.51	Benign	0.24	Tolerated	3.77	5	1	-1	-0.3	-22.05
c.3607C>T	H1203Y	Coiled-coil				6-33446599-C-T	2	1.24e-6	-6.834	Likely Benign	0.149	Likely Benign	Likely Benign	0.233	Likely Benign										-1.52	Neutral	0.006	Benign	0.011	Benign	5.55	Benign	0.10	Tolerated	3.77	5	2	0	1.9	26.03
c.3611C>T	S1204L	Coiled-coil				6-33446603-C-T	1	6.20e-7	-4.672	Likely Benign	0.325	Likely Benign	Likely Benign	0.375	Likely Benign										-0.86	Neutral	0.035	Benign	0.028	Benign	5.35	Benign	0.32	Tolerated	3.77	5	-2	-3	4.6	26.08
c.3614T>C	L1205P	Coiled-coil	Uncertain		1				-16.878	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.536	Likely Pathogenic										-5.91	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.45	Pathogenic	0.00	Affected			-3	-3	-5.4	-16.04
c.3622C>T	R1208W	Coiled-coil				6-33446614-C-T	1	6.20e-7	-12.124	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.192	Likely Benign										-5.53	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.47	Pathogenic	0.00	Affected	3.77	5	-3	2	3.6	30.03
c.362C>G	A121G					6-33432227-C-G	4	2.48e-6	-3.123	Likely Benign	0.099	Likely Benign	Likely Benign	0.073	Likely Benign										-0.52	Neutral	0.118	Benign	0.026	Benign	4.06	Benign	0.07	Tolerated	3.61	5	0	1	-2.2	-14.03
c.362C>T	A121V					6-33432227-C-T	3	1.86e-6	-3.818	Likely Benign	0.086	Likely Benign	Likely Benign	0.046	Likely Benign										-1.44	Neutral	0.213	Benign	0.050	Benign	4.04	Benign	0.02	Affected	3.61	5	0	0	2.4	28.05
c.3631A>G	M1211V	Coiled-coil				6-33446623-A-G	3	1.86e-6	-2.101	Likely Benign	0.258	Likely Benign	Likely Benign	0.412	Likely Benign										-0.29	Neutral	0.932	Possibly Damaging	0.949	Probably Damaging	5.43	Benign	0.72	Tolerated	3.77	5	1	2	2.3	-32.06
c.3632T>A	M1211K	Coiled-coil	Likely Benign		1				-9.013	Likely Pathogenic	0.662	Likely Pathogenic	Likely Benign	0.595	Likely Pathogenic										-2.95	Deleterious	0.987	Probably Damaging	0.979	Probably Damaging	5.59	Benign	0.01	Affected	3.77	5	0	-1	-5.8	-3.02
c.3633G>A	M1211I	Coiled-coil				6-33446625-G-A	3	1.86e-6	-1.537	Likely Benign	0.764	Likely Pathogenic	Likely Benign	0.298	Likely Benign										-0.42	Neutral	0.969	Probably Damaging	0.968	Probably Damaging	5.40	Benign	1.00	Tolerated	3.77	5	1	2	2.6	-18.03
c.3635C>T	S1212F	Coiled-coil	Conflicting		2				-14.445	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.271	Likely Benign										-4.52	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	2.03	Pathogenic	0.00	Affected	3.77	5	-3	-2	3.6	60.10
c.3638A>C	N1213T	Coiled-coil	Conflicting		2	6-33446630-A-C	46	2.85e-5	-5.428	Likely Benign	0.266	Likely Benign	Likely Benign	0.097	Likely Benign										-1.08	Neutral	0.959	Probably Damaging	0.721	Possibly Damaging	2.74	Benign	1.00	Tolerated	3.77	5	0	0	2.8	-13.00
c.3638A>G	N1213S	Coiled-coil	Benign		1	6-33446630-A-G	13	8.05e-6	-4.086	Likely Benign	0.081	Likely Benign	Likely Benign	0.094	Likely Benign										-0.56	Neutral	0.906	Possibly Damaging	0.551	Possibly Damaging	2.82	Benign	0.68	Tolerated	3.77	5	1	1	2.7	-27.03																10.1016/j.ajhg.2020.11.011
c.3640C>G	R1214G	Coiled-coil				6-33446632-C-G	1	6.20e-7	-9.697	Likely Pathogenic	0.725	Likely Pathogenic	Likely Benign	0.131	Likely Benign										-4.41	Deleterious	0.992	Probably Damaging	0.828	Possibly Damaging	2.48	Pathogenic	0.01	Affected	3.77	5	-2	-3	4.1	-99.14
c.3640C>T	R1214W	Coiled-coil	Uncertain		1	6-33446632-C-T	2	1.24e-6	-8.799	Likely Pathogenic	0.710	Likely Pathogenic	Likely Benign	0.143	Likely Benign										-4.95	Deleterious	1.000	Probably Damaging	0.983	Probably Damaging	2.45	Pathogenic	0.00	Affected	3.77	5	2	-3	3.6	30.03
c.3641G>A	R1214Q	Coiled-coil				6-33446633-G-A	6	3.72e-6	-6.059	Likely Benign	0.138	Likely Benign	Likely Benign	0.078	Likely Benign										-1.69	Neutral	0.993	Probably Damaging	0.738	Possibly Damaging	2.65	Benign	0.02	Affected	3.77	5	1	1	1.0	-28.06
c.364C>T	P122S					6-33432229-C-T	1	6.20e-7	-3.389	Likely Benign	0.098	Likely Benign	Likely Benign	0.091	Likely Benign										-1.13	Neutral	0.036	Benign	0.025	Benign	4.22	Benign	0.31	Tolerated	3.61	5	-1	1	0.8	-10.04
c.3650A>G	E1217G	Coiled-coil				6-33446642-A-G			-10.803	Likely Pathogenic	0.620	Likely Pathogenic	Likely Benign	0.331	Likely Benign										-5.38	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	2.35	Pathogenic	0.00	Affected	3.77	5	-2	0	3.1	-72.06
c.3653A>T	E1218V	Coiled-coil	Uncertain		2				-5.647	Likely Benign	0.936	Likely Pathogenic	Ambiguous	0.418	Likely Benign										-5.68	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.21	Pathogenic	0.00	Affected	3.77	5	-2	-2	7.7	-29.98
c.3655T>C	Y1219H	Coiled-coil	Uncertain		1				-9.511	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.363	Likely Benign										-3.62	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.15	Pathogenic	0.00	Affected	3.77	5	0	2	-1.9	-26.03
c.3658G>A	E1220K	Coiled-coil				6-33446650-G-A	1	6.20e-7	-12.478	Likely Pathogenic	0.988	Likely Pathogenic	Likely Pathogenic	0.415	Likely Benign										-3.46	Deleterious	0.999	Probably Damaging	0.995	Probably Damaging	1.63	Pathogenic	0.00	Affected	3.77	5	1	0	-0.4	-0.94
c.3661C>T	R1221W	Coiled-coil	Conflicting		3	6-33446653-C-T	1	6.20e-7	-10.938	Likely Pathogenic	0.651	Likely Pathogenic	Likely Benign	0.174	Likely Benign										-4.57	Deleterious	1.000	Probably Damaging	0.987	Probably Damaging	2.50	Benign	0.01	Affected	3.77	5	2	-3	3.6	30.03
c.3662G>A	R1221Q	Coiled-coil	Conflicting		2	6-33446654-G-A	4	2.48e-6	-5.491	Likely Benign	0.115	Likely Benign	Likely Benign	0.078	Likely Benign										-1.46	Neutral	0.836	Possibly Damaging	0.153	Benign	2.56	Benign	0.12	Tolerated	3.77	5	1	1	1.0	-28.06
c.3671T>G	L1224R	Coiled-coil				6-33446663-T-G	1	6.20e-7	-7.504	In-Between	0.220	Likely Benign	Likely Benign	0.113	Likely Benign										-1.85	Neutral	0.989	Probably Damaging	0.900	Possibly Damaging	2.42	Pathogenic	0.33	Tolerated	3.77	5	-2	-3	-8.3	43.03
c.3686A>C	Q1229P	Coiled-coil	Uncertain		1				-10.397	Likely Pathogenic	0.980	Likely Pathogenic	Likely Pathogenic	0.422	Likely Benign										-3.69	Deleterious	0.998	Probably Damaging	0.995	Probably Damaging	1.75	Pathogenic	0.12	Tolerated	3.77	5	0	-1	1.9	-31.01
c.36C>A	S12R					6-33420300-C-A			-4.033	Likely Benign	0.499	Ambiguous	Likely Benign	0.097	Likely Benign										-0.30	Neutral	0.000	Benign	0.000	Benign	4.09	Benign	0.00	Affected	4.32	1	0	-1	-3.7	69.11
c.36C>G	S12R		Uncertain		1	6-33420300-C-G	4	2.59e-6	-4.033	Likely Benign	0.499	Ambiguous	Likely Benign	0.097	Likely Benign										-0.30	Neutral	0.000	Benign	0.000	Benign	4.09	Benign	0.00	Affected	4.32	1	0	-1	-3.7	69.11
c.3705G>A	M1235I	Coiled-coil	Uncertain		1				-4.312	Likely Benign	0.310	Likely Benign	Likely Benign	0.027	Likely Benign										-1.44	Neutral	0.139	Benign	0.056	Benign	2.69	Benign	0.04	Affected	3.77	5	1	2	2.6	-18.03
c.3705G>C	M1235I	Coiled-coil				6-33446697-G-C	1	6.20e-7	-4.312	Likely Benign	0.310	Likely Benign	Likely Benign	0.027	Likely Benign										-1.44	Neutral	0.139	Benign	0.056	Benign	2.69	Benign	0.04	Affected	3.77	5	1	2	2.6	-18.03
c.370G>A	A124T					6-33432235-G-A	1	6.20e-7	-3.551	Likely Benign	0.101	Likely Benign	Likely Benign	0.046	Likely Benign										-0.26	Neutral	0.734	Possibly Damaging	0.187	Benign	4.17	Benign	0.78	Tolerated	3.61	5	0	1	-2.5	30.03
c.3710A>G	Y1237C	Coiled-coil				6-33446702-A-G	1	6.20e-7	-8.600	Likely Pathogenic	0.992	Likely Pathogenic	Likely Pathogenic	0.429	Likely Benign										-7.15	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.43	Pathogenic	0.00	Affected	3.77	5	-2	0	3.8	-60.04
c.3714G>C	Q1238H	Coiled-coil				6-33446706-G-C	1	6.20e-7	-8.647	Likely Pathogenic	0.757	Likely Pathogenic	Likely Benign	0.202	Likely Benign										-3.49	Deleterious	0.998	Probably Damaging	0.996	Probably Damaging	2.31	Pathogenic	0.01	Affected	3.77	5	0	3	0.3	9.01
c.3719G>A	R1240Q	Coiled-coil				6-33446711-G-A	2	1.24e-6	-7.110	In-Between	0.717	Likely Pathogenic	Likely Benign	0.304	Likely Benign										-3.09	Deleterious	0.999	Probably Damaging	0.994	Probably Damaging	1.69	Pathogenic	0.00	Affected	3.77	5	1	1	1.0	-28.06
c.371C>T	A124V		Conflicting		2	6-33432236-C-T	9	5.58e-6	-4.259	Likely Benign	0.138	Likely Benign	Likely Benign	0.073	Likely Benign										-1.52	Neutral	0.173	Benign	0.009	Benign	4.07	Benign	0.03	Affected	3.61	5	0	0	2.4	28.05
c.3724G>A	E1242K	Coiled-coil				6-33446716-G-A	1	6.20e-7	-10.075	Likely Pathogenic	0.798	Likely Pathogenic	Ambiguous	0.179	Likely Benign										-3.13	Deleterious	0.939	Possibly Damaging	0.670	Possibly Damaging	2.22	Pathogenic	0.00	Affected	3.77	5	1	0	-0.4	-0.94
c.3727C>A	Q1243K	Coiled-coil				6-33446719-C-A	1	6.20e-7	-7.110	In-Between	0.230	Likely Benign	Likely Benign	0.050	Likely Benign										-1.39	Neutral	0.679	Possibly Damaging	0.446	Benign	2.72	Benign	0.08	Tolerated	3.77	5	1	1	-0.4	0.04
c.3728A>G	Q1243R	Coiled-coil				6-33446720-A-G	1	6.20e-7	-7.131	In-Between	0.225	Likely Benign	Likely Benign	0.127	Likely Benign										-1.99	Neutral	0.912	Possibly Damaging	0.629	Possibly Damaging	2.67	Benign	0.02	Affected	3.77	5	1	1	-1.0	28.06
c.3729G>C	Q1243H	Coiled-coil				6-33446721-G-C	1	6.19e-7	-5.281	Likely Benign	0.204	Likely Benign	Likely Benign	0.107	Likely Benign										-1.90	Neutral	0.991	Probably Damaging	0.897	Possibly Damaging	2.65	Benign	0.02	Affected	3.77	5	0	3	0.3	9.01
c.3731G>A	S1244N	Coiled-coil	Uncertain		1				-9.008	Likely Pathogenic	0.751	Likely Pathogenic	Likely Benign	0.154	Likely Benign										-1.87	Neutral	0.997	Probably Damaging	0.992	Probably Damaging	2.10	Pathogenic	0.15	Tolerated	3.77	5	1	1	-2.7	27.03
c.3737A>G	K1246R	Coiled-coil				6-33446729-A-G	1	6.20e-7	-2.444	Likely Benign	0.097	Likely Benign	Likely Benign	0.026	Likely Benign										-0.86	Neutral	0.031	Benign	0.017	Benign	2.66	Benign	0.04	Affected	3.77	5	2	3	-0.6	28.01
c.373C>T	P125S		Uncertain		1				-3.769	Likely Benign	0.238	Likely Benign	Likely Benign	0.121	Likely Benign										-3.57	Deleterious	0.580	Possibly Damaging	0.140	Benign	2.86	Benign	0.02	Affected	3.61	5	1	-1	0.8	-10.04
c.3740G>A	R1247K	Coiled-coil				6-33446732-G-A	4	2.48e-6	-4.713	Likely Benign	0.179	Likely Benign	Likely Benign	0.082	Likely Benign										-2.39	Neutral	0.122	Benign	0.064	Benign	1.80	Pathogenic	0.00	Affected	3.77	5	2	3	0.6	-28.01
c.3751C>A	Q1251K	Coiled-coil				6-33446743-C-A	1	6.20e-7	-11.113	Likely Pathogenic	0.850	Likely Pathogenic	Ambiguous	0.208	Likely Benign										-2.92	Deleterious	0.985	Probably Damaging	0.981	Probably Damaging	2.53	Benign	0.00	Affected	3.77	5	1	1	-0.4	0.04
c.3773A>G	Q1258R	Coiled-coil	Uncertain		1				-10.971	Likely Pathogenic	0.931	Likely Pathogenic	Ambiguous	0.316	Likely Benign										-3.19	Deleterious	0.994	Probably Damaging	0.988	Probably Damaging	2.00	Pathogenic	0.00	Affected			1	1	-1.0	28.06
c.3777C>G	I1259M	Coiled-coil				6-33446769-C-G	2	1.24e-6	-5.177	Likely Benign	0.447	Ambiguous	Likely Benign	0.227	Likely Benign										1.35	Neutral	0.999	Probably Damaging	0.998	Probably Damaging	2.87	Benign	1.00	Tolerated	3.77	5	1	2	-2.6	18.03
c.3778A>C	K1260Q	Coiled-coil				6-33446770-A-C			-7.830	In-Between	0.325	Likely Benign	Likely Benign	0.367	Likely Benign										-3.06	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.36	Pathogenic	0.00	Affected	3.77	5	1	1	0.4	-0.04
c.3779A>G	K1260R	Coiled-coil				6-33446771-A-G	1	6.20e-7	-6.033	Likely Benign	0.135	Likely Benign	Likely Benign	0.254	Likely Benign										-2.29	Neutral	0.999	Probably Damaging	0.995	Probably Damaging	2.40	Pathogenic	0.00	Affected	3.77	5	2	3	-0.6	28.01
c.3788T>C	I1263T	Coiled-coil	Uncertain		1	6-33446780-T-C	2	1.24e-6	-6.564	Likely Benign	0.962	Likely Pathogenic	Likely Pathogenic	0.529	Likely Pathogenic										-4.15	Deleterious	0.946	Possibly Damaging	0.673	Possibly Damaging	1.81	Pathogenic	0.00	Affected	3.77	5	0	-1	-5.2	-12.05
c.3794G>C	R1265T	Coiled-coil	Likely Pathogenic		1				-10.129	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.529	Likely Pathogenic										-4.97	Deleterious	0.997	Probably Damaging	0.994	Probably Damaging	2.29	Pathogenic	0.00	Affected	3.77	5	-1	-1	3.8	-55.08
c.3797T>C	L1266P	Coiled-coil				6-33447845-T-C			-16.566	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.424	Likely Benign										-5.83	Deleterious	0.999	Probably Damaging	0.977	Probably Damaging	2.10	Pathogenic	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.37A>G	I13V		Uncertain		1				-2.497	Likely Benign	0.105	Likely Benign	Likely Benign	0.110	Likely Benign										0.01	Neutral	0.000	Benign	0.000	Benign	4.25	Benign	0.00	Affected			4	3	-0.3	-14.03
c.3802C>A	L1268M	Coiled-coil				6-33447850-C-A			-4.689	Likely Benign	0.140	Likely Benign	Likely Benign	0.062	Likely Benign										-0.07	Neutral	0.990	Probably Damaging	0.796	Possibly Damaging	2.67	Benign	0.08	Tolerated	3.77	5	2	4	-1.9	18.03
c.3806T>A	V1269E	Coiled-coil	Uncertain		1				-11.418	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.403	Likely Benign										-5.05	Deleterious	0.999	Probably Damaging	0.995	Probably Damaging	2.09	Pathogenic	0.00	Affected	3.77	5	-2	-2	-7.7	29.98
c.3809A>G	E1270G	Coiled-coil				6-33447857-A-G			-12.022	Likely Pathogenic	0.971	Likely Pathogenic	Likely Pathogenic	0.385	Likely Benign										-5.90	Deleterious	0.999	Probably Damaging	0.992	Probably Damaging	2.05	Pathogenic	0.00	Affected	3.77	5	-2	0	3.1	-72.06
c.380G>A	R127Q		Uncertain		1	6-33432245-G-A	6	3.72e-6	-1.711	Likely Benign	0.320	Likely Benign	Likely Benign	0.037	Likely Benign										-1.04	Neutral	0.006	Benign	0.001	Benign	4.04	Benign	0.02	Affected	3.74	4	1	1	1.0	-28.06
c.3810G>T	E1270D	Coiled-coil				6-33447858-G-T			-9.379	Likely Pathogenic	0.978	Likely Pathogenic	Likely Pathogenic	0.219	Likely Benign										-2.53	Deleterious	0.992	Probably Damaging	0.983	Probably Damaging	2.26	Pathogenic	0.00	Affected			3	2	0.0	-14.03
c.3812A>G	E1271G					6-33447860-A-G			-4.857	Likely Benign	0.393	Ambiguous	Likely Benign	0.288	Likely Benign										-5.37	Deleterious	0.905	Possibly Damaging	0.538	Possibly Damaging	2.05	Pathogenic	0.00	Affected	3.77	5	-2	0	3.1	-72.06																10.1016/j.ajhg.2020.11.011
c.3814G>C	E1272Q					6-33447862-G-C	1	6.45e-7	-3.000	Likely Benign	0.651	Likely Pathogenic	Likely Benign	0.207	Likely Benign										-2.53	Deleterious	0.997	Probably Damaging	0.992	Probably Damaging	2.25	Pathogenic	0.00	Affected	3.77	5	2	2	0.0	-0.98
c.3815A>G	E1272G					6-33447863-A-G			-1.919	Likely Benign	0.863	Likely Pathogenic	Ambiguous	0.287	Likely Benign										-5.89	Deleterious	0.999	Probably Damaging	0.992	Probably Damaging	2.22	Pathogenic	0.00	Affected	3.77	5	-2	0	3.1	-72.06
c.3816G>T	E1272D					6-33447864-G-T			-4.781	Likely Benign	0.751	Likely Pathogenic	Likely Benign	0.188	Likely Benign										-2.53	Deleterious	0.992	Probably Damaging	0.983	Probably Damaging	2.27	Pathogenic	0.00	Affected	3.77	5	2	3	0.0	-14.03
c.3817C>A	L1273M					6-33447865-C-A			-5.375	Likely Benign	0.503	Ambiguous	Likely Benign	0.161	Likely Benign										-1.68	Neutral	0.983	Probably Damaging	0.874	Possibly Damaging	2.14	Pathogenic	0.00	Affected	3.77	5	2	4	-1.9	18.03
c.3818T>C	L1273P					6-33447866-T-C			-9.443	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.523	Likely Pathogenic										-5.87	Deleterious	0.997	Probably Damaging	0.950	Probably Damaging	2.12	Pathogenic	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.3820C>A	R1274S					6-33447868-C-A			-3.149	Likely Benign	0.830	Likely Pathogenic	Ambiguous	0.139	Likely Benign										-3.19	Deleterious	0.997	Probably Damaging	0.993	Probably Damaging	2.52	Benign	0.01	Affected	3.77	5	-1	0	3.7	-69.11
c.3820C>T	R1274C		Uncertain		1	6-33447868-C-T			-6.467	Likely Benign	0.439	Ambiguous	Likely Benign	0.170	Likely Benign										-5.22	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	2.46	Pathogenic	0.00	Affected	3.77	5	-4	-3	7.0	-53.05
c.3821G>A	R1274H		Likely Benign		1	6-33447869-G-A	4	2.58e-6	-5.259	Likely Benign	0.256	Likely Benign	Likely Benign	0.149	Likely Benign										-3.20	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	2.49	Pathogenic	0.01	Affected	3.77	5	0	2	1.3	-19.05
c.3823C>T	R1275W					6-33447871-C-T	3	1.93e-6	-9.895	Likely Pathogenic	0.513	Ambiguous	Likely Benign	0.161	Likely Benign										-4.76	Deleterious	0.999	Probably Damaging	0.875	Possibly Damaging	2.51	Benign	0.00	Affected	3.77	5	-3	2	3.6	30.03
c.3824G>A	R1275Q		Uncertain		1	6-33447872-G-A	2	1.29e-6	-4.928	Likely Benign	0.121	Likely Benign	Likely Benign	0.103	Likely Benign										-1.72	Neutral	0.898	Possibly Damaging	0.147	Benign	2.59	Benign	0.03	Affected	3.77	5	1	1	1.0	-28.06
c.3824G>C	R1275P					6-33447872-G-C			-7.155	In-Between	0.823	Likely Pathogenic	Ambiguous	0.145	Likely Benign										-3.55	Deleterious	0.966	Probably Damaging	0.651	Possibly Damaging	2.53	Benign	0.01	Affected	3.77	5	-2	0	2.9	-59.07
c.3824G>T	R1275L		Likely Benign		1	6-33447872-G-T	1	6.45e-7	-6.052	Likely Benign	0.446	Ambiguous	Likely Benign	0.117	Likely Benign										-4.04	Deleterious	0.800	Possibly Damaging	0.277	Benign	2.55	Benign	0.01	Affected	3.77	5	-3	-2	8.3	-43.03
c.3826G>T	D1276Y					6-33447874-G-T			-1.558	Likely Benign	0.768	Likely Pathogenic	Likely Benign	0.325	Likely Benign										-6.66	Deleterious	0.999	Probably Damaging	0.928	Probably Damaging	1.18	Pathogenic	0.00	Affected	3.77	5	-3	-4	2.2	48.09
c.3828C>A	D1276E					6-33447876-C-A			-0.388	Likely Benign	0.416	Ambiguous	Likely Benign	0.091	Likely Benign										-2.64	Deleterious	0.027	Benign	0.020	Benign	1.26	Pathogenic	0.00	Affected	3.77	5	2	3	0.0	14.03
c.3829C>A	H1277N					6-33447877-C-A			-3.347	Likely Benign	0.193	Likely Benign	Likely Benign	0.114	Likely Benign										-4.96	Deleterious	0.224	Benign	0.120	Benign	2.14	Pathogenic	0.00	Affected	3.77	5	1	2	-0.3	-23.04
c.3829C>G	H1277D					6-33447877-C-G			-4.632	Likely Benign	0.536	Ambiguous	Likely Benign	0.172	Likely Benign										-6.38	Deleterious	0.411	Benign	0.091	Benign	2.14	Pathogenic	0.00	Affected	3.77	5	-1	1	-0.3	-22.05
c.382C>A	P128T		Uncertain		1	6-33432247-C-A	1	6.20e-7	-4.217	Likely Benign	0.267	Likely Benign	Likely Benign	0.075	Likely Benign										-0.96	Neutral	0.952	Possibly Damaging	0.500	Possibly Damaging	4.19	Benign	0.35	Tolerated	3.74	4	-1	0	0.9	3.99
c.382C>T	P128S					6-33432247-C-T	1	6.20e-7	-3.234	Likely Benign	0.268	Likely Benign	Likely Benign	0.084	Likely Benign										-1.35	Neutral	0.734	Possibly Damaging	0.243	Benign	4.20	Benign	0.24	Tolerated	3.74	4	-1	1	0.8	-10.04
c.3830A>C	H1277P					6-33447878-A-C			-3.829	Likely Benign	0.324	Likely Benign	Likely Benign	0.237	Likely Benign										-7.14	Deleterious	0.586	Possibly Damaging	0.287	Benign	2.12	Pathogenic	0.00	Affected	3.77	5	-2	0	1.6	-40.02
c.3831C>A	H1277Q					6-33447879-C-A			-3.323	Likely Benign	0.325	Likely Benign	Likely Benign	0.078	Likely Benign										-5.34	Deleterious	0.004	Benign	0.010	Benign	2.14	Pathogenic	0.00	Affected	3.77	5	0	3	-0.3	-9.01
c.3832C>A	P1278T					6-33447880-C-A			-5.505	Likely Benign	0.095	Likely Benign	Likely Benign	0.064	Likely Benign										-0.60	Neutral	0.059	Benign	0.026	Benign	2.73	Benign	0.11	Tolerated	3.77	5	-1	0	0.9	3.99
c.3833C>A	P1278H					6-33447881-C-A	7	4.51e-6	-5.691	Likely Benign	0.142	Likely Benign	Likely Benign	0.087	Likely Benign										-1.69	Neutral	0.938	Possibly Damaging	0.477	Possibly Damaging	2.67	Benign	0.01	Affected	3.77	5	-2	0	-1.6	40.02
c.3835G>A	A1279T		Uncertain		2	6-33447883-G-A	2	1.29e-6	-4.871	Likely Benign	0.071	Likely Benign	Likely Benign	0.178	Likely Benign										-0.30	Neutral	0.001	Benign	0.000	Benign	2.71	Benign	0.09	Tolerated	3.77	5	1	0	-2.5	30.03
c.3835G>T	A1279S					6-33447883-G-T			-4.281	Likely Benign	0.073	Likely Benign	Likely Benign	0.134	Likely Benign										0.37	Neutral	0.019	Benign	0.019	Benign	2.74	Benign	0.16	Tolerated	3.77	5	1	1	-2.6	16.00
c.3836C>A	A1279D					6-33447884-C-A			-3.914	Likely Benign	0.172	Likely Benign	Likely Benign	0.087	Likely Benign										1.38	Neutral	0.000	Benign	0.000	Benign	2.89	Benign	0.35	Tolerated	3.77	5	-2	0	-5.3	44.01
c.3836C>T	A1279V					6-33447884-C-T			-4.892	Likely Benign	0.088	Likely Benign	Likely Benign	0.049	Likely Benign										-1.23	Neutral	0.017	Benign	0.017	Benign	2.68	Benign	0.07	Tolerated	3.77	5	0	0	2.4	28.05
c.3839T>C	M1280T					6-33447887-T-C	3	1.93e-6	-2.305	Likely Benign	0.112	Likely Benign	Likely Benign	0.158	Likely Benign										-2.26	Neutral	0.369	Benign	0.120	Benign	2.34	Pathogenic	0.00	Affected	3.77	5	-1	-1	-2.6	-30.09
c.383C>T	P128L					6-33432248-C-T	1	6.20e-7	-4.791	Likely Benign	0.541	Ambiguous	Likely Benign	0.087	Likely Benign										-0.47	Neutral	0.952	Possibly Damaging	0.500	Possibly Damaging	4.20	Benign	0.38	Tolerated	3.74	4	-3	-3	5.4	16.04
c.3841G>A	A1281T					6-33447889-G-A	1	6.44e-7	-4.366	Likely Benign	0.074	Likely Benign	Likely Benign	0.090	Likely Benign										-0.68	Neutral	0.818	Possibly Damaging	0.355	Benign	2.67	Benign	0.16	Tolerated	4.32	4	0	1	-2.5	30.03
c.3841G>T	A1281S					6-33447889-G-T			-4.175	Likely Benign	0.080	Likely Benign	Likely Benign	0.081	Likely Benign										-0.22	Neutral	0.649	Possibly Damaging	0.266	Benign	2.69	Benign	0.33	Tolerated	4.32	4	1	1	-2.6	16.00
c.3842C>A	A1281D					6-33447890-C-A			-5.183	Likely Benign	0.178	Likely Benign	Likely Benign	0.054	Likely Benign										-0.76	Neutral	0.901	Possibly Damaging	0.516	Possibly Damaging	2.68	Benign	0.15	Tolerated	4.32	4	-2	0	-5.3	44.01
c.3842C>T	A1281V					6-33447890-C-T			-4.021	Likely Benign	0.088	Likely Benign	Likely Benign	0.037	Likely Benign										-0.79	Neutral	0.057	Benign	0.026	Benign	2.65	Benign	0.15	Tolerated	4.32	4	0	0	2.4	28.05
c.3844G>A	E1282K					6-33447892-G-A			-3.805	Likely Benign	0.226	Likely Benign	Likely Benign	0.173	Likely Benign										-1.17	Neutral	0.126	Benign	0.026	Benign	2.73	Benign	0.16	Tolerated	3.77	5	1	0	-0.4	-0.94
c.3845A>G	E1282G					6-33447893-A-G			-2.649	Likely Benign	0.104	Likely Benign	Likely Benign	0.219	Likely Benign										-1.25	Neutral	0.000	Benign	0.001	Benign	2.68	Benign	0.00	Affected			0	-2	3.1	-72.06
c.3845A>T	E1282V					6-33447893-A-T			-2.790	Likely Benign	0.190	Likely Benign	Likely Benign	0.102	Likely Benign										-1.71	Neutral	0.369	Benign	0.078	Benign	2.72	Benign	0.04	Affected			-2	-2	7.7	-29.98
c.3846G>C	E1282D		Uncertain		1	6-33447894-G-C	1	6.44e-7	-3.879	Likely Benign	0.074	Likely Benign	Likely Benign	0.104	Likely Benign										-1.26	Neutral	0.112	Benign	0.036	Benign	2.70	Benign	0.39	Tolerated	3.77	5	3	2	0.0	-14.03
c.3846G>T	E1282D					6-33447894-G-T			-3.879	Likely Benign	0.074	Likely Benign	Likely Benign	0.104	Likely Benign										-1.26	Neutral	0.112	Benign	0.036	Benign	2.70	Benign	0.39	Tolerated	3.77	5	3	2	0.0	-14.03
c.3847C>A	P1283T					6-33447895-C-A			-4.781	Likely Benign	0.064	Likely Benign	Likely Benign	0.071	Likely Benign										-0.45	Neutral	0.451	Benign	0.193	Benign	2.76	Benign	0.11	Tolerated	3.77	5	-1	0	0.9	3.99
c.3847C>T	P1283S					6-33447895-C-T			-4.289	Likely Benign	0.072	Likely Benign	Likely Benign	0.040	Likely Benign										0.06	Neutral	0.292	Benign	0.110	Benign	2.86	Benign	0.30	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3848C>A	P1283Q					6-33447896-C-A			-4.028	Likely Benign	0.085	Likely Benign	Likely Benign	0.102	Likely Benign										-1.11	Neutral	0.991	Probably Damaging	0.567	Possibly Damaging	2.72	Benign	0.04	Affected	3.77	5	-1	0	-1.9	31.01
c.3848C>T	P1283L		Benign		1	6-33447896-C-T	32	2.06e-5	-3.740	Likely Benign	0.093	Likely Benign	Likely Benign	0.047	Likely Benign										-1.04	Neutral	0.005	Benign	0.003	Benign	2.76	Benign	0.06	Tolerated	3.77	5	-3	-3	5.4	16.04
c.3850C>A	L1284M					6-33447898-C-A			-5.332	Likely Benign	0.104	Likely Benign	Likely Benign	0.044	Likely Benign										-0.49	Neutral	0.970	Probably Damaging	0.637	Possibly Damaging	2.61	Benign	0.03	Affected	3.77	5	2	4	-1.9	18.03
c.3851T>C	L1284P					6-33447899-T-C			-2.451	Likely Benign	0.076	Likely Benign	Likely Benign	0.191	Likely Benign										-3.05	Deleterious	0.990	Probably Damaging	0.722	Possibly Damaging	2.48	Pathogenic	0.01	Affected	3.77	5	-3	-3	-5.4	-16.04
c.3853C>A	P1285T					6-33447901-C-A			-4.230	Likely Benign	0.078	Likely Benign	Likely Benign	0.047	Likely Benign										-0.35	Neutral	0.451	Benign	0.193	Benign	4.33	Benign	0.40	Tolerated	4.32	2	-1	0	0.9	3.99
c.3853C>T	P1285S					6-33447901-C-T	1	6.44e-7	-3.875	Likely Benign	0.086	Likely Benign	Likely Benign	0.035	Likely Benign										-1.27	Neutral	0.802	Possibly Damaging	0.249	Benign	4.34	Benign	0.29	Tolerated	4.32	2	-1	1	0.8	-10.04
c.3854C>A	P1285Q					6-33447902-C-A			-4.073	Likely Benign	0.100	Likely Benign	Likely Benign	0.072	Likely Benign										-1.67	Neutral	0.977	Probably Damaging	0.632	Possibly Damaging	4.22	Benign	0.13	Tolerated	4.32	2	-1	0	-1.9	31.01
c.3854C>G	P1285R					6-33447902-C-G			-3.417	Likely Benign	0.157	Likely Benign	Likely Benign	0.094	Likely Benign										-2.10	Neutral	0.977	Probably Damaging	0.632	Possibly Damaging	4.22	Benign	0.14	Tolerated	4.32	2	-2	0	-2.9	59.07
c.3856G>A	E1286K					6-33447904-G-A			-3.784	Likely Benign	0.395	Ambiguous	Likely Benign	0.195	Likely Benign										-2.36	Neutral	0.770	Possibly Damaging	0.242	Benign	2.47	Pathogenic	0.02	Affected	3.77	5	1	0	-0.4	-0.94
c.3858A>T	E1286D		Conflicting		4	6-33447906-A-T	143	9.22e-5	-4.010	Likely Benign	0.081	Likely Benign	Likely Benign	0.036	Likely Benign										1.02	Neutral	0.001	Benign	0.004	Benign	2.96	Benign	1.00	Tolerated	3.77	5	3	2	0.0	-14.03																10.1016/j.ajhg.2020.11.011
c.3859C>A	P1287T					6-33447907-C-A			-3.940	Likely Benign	0.077	Likely Benign	Likely Benign	0.044	Likely Benign										-0.22	Neutral	0.126	Benign	0.041	Benign	2.78	Benign	0.04	Affected	3.77	5	-1	0	0.9	3.99
c.3859C>T	P1287S					6-33447907-C-T			-3.258	Likely Benign	0.090	Likely Benign	Likely Benign	0.055	Likely Benign										0.70	Neutral	0.004	Benign	0.004	Benign	2.96	Benign	0.96	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3860C>A	P1287H					6-33447908-C-A			-3.606	Likely Benign	0.135	Likely Benign	Likely Benign	0.043	Likely Benign										-1.36	Neutral	0.938	Possibly Damaging	0.596	Possibly Damaging	2.80	Benign	0.00	Affected	3.77	5	-2	0	-1.6	40.02
c.3860C>T	P1287L		Conflicting		2	6-33447908-C-T			-2.800	Likely Benign	0.117	Likely Benign	Likely Benign	0.061	Likely Benign										-1.66	Neutral	0.021	Benign	0.017	Benign	2.76	Benign	0.02	Affected	3.77	5	-3	-3	5.4	16.04
c.3862A>G	K1288E		Uncertain		1	6-33447910-A-G	5	3.22e-6	-2.751	Likely Benign	0.407	Ambiguous	Likely Benign	0.185	Likely Benign										-3.27	Deleterious	0.979	Probably Damaging	0.973	Probably Damaging	2.13	Pathogenic	0.00	Affected	3.77	5	1	0	0.4	0.94
c.386C>T	S129L					6-33432251-C-T	1	6.20e-7	-4.487	Likely Benign	0.456	Ambiguous	Likely Benign	0.256	Likely Benign										-0.18	Neutral	0.000	Benign	0.000	Benign	4.14	Benign	0.05	Affected	3.74	4	-2	-3	4.6	26.08
c.3871C>A	L1291M					6-33447919-C-A			-5.625	Likely Benign	0.159	Likely Benign	Likely Benign	0.045	Likely Benign										-0.93	Neutral	0.970	Probably Damaging	0.728	Possibly Damaging	2.53	Benign	0.03	Affected	3.77	5	2	4	-1.9	18.03
c.3872T>G	L1291R					6-33447920-T-G	1	6.44e-7	-3.977	Likely Benign	0.302	Likely Benign	Likely Benign	0.287	Likely Benign										-4.29	Deleterious	0.990	Probably Damaging	0.856	Possibly Damaging	2.49	Pathogenic	0.00	Affected	3.77	5	-2	-3	-8.3	43.03
c.3874C>T	L1292F					6-33447922-C-T			-5.759	Likely Benign	0.200	Likely Benign	Likely Benign	0.097	Likely Benign										-1.88	Neutral	0.611	Possibly Damaging	0.329	Benign	2.49	Pathogenic	0.03	Affected	3.77	5	0	2	-1.0	34.02
c.3875T>A	L1292H					6-33447923-T-A			-5.692	Likely Benign	0.335	Likely Benign	Likely Benign	0.202	Likely Benign										-4.42	Deleterious	0.992	Probably Damaging	0.820	Possibly Damaging	2.46	Pathogenic	0.00	Affected	3.77	5	-3	-2	-7.0	23.98
c.3877G>A	D1293N					6-33447925-G-A	5	3.22e-6	-3.983	Likely Benign	0.237	Likely Benign	Likely Benign	0.175	Likely Benign										-3.30	Deleterious	0.950	Possibly Damaging	0.414	Benign	2.33	Pathogenic	0.00	Affected	3.77	5	1	2	0.0	-0.98
c.3879C>A	D1293E					6-33447927-C-A			-2.627	Likely Benign	0.136	Likely Benign	Likely Benign	0.042	Likely Benign										-1.86	Neutral	0.011	Benign	0.008	Benign	2.39	Pathogenic	0.00	Affected	3.77	5	2	3	0.0	14.03
c.3880G>A	A1294T					6-33447928-G-A			-3.966	Likely Benign	0.093	Likely Benign	Likely Benign	0.290	Likely Benign										-3.04	Deleterious	0.999	Probably Damaging	0.989	Probably Damaging	2.18	Pathogenic	0.00	Affected	3.77	5	0	1	-2.5	30.03
c.3880G>C	A1294P					6-33447928-G-C	1	6.45e-7	-2.688	Likely Benign	0.220	Likely Benign	Likely Benign	0.367	Likely Benign										-3.79	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	2.14	Pathogenic	0.00	Affected	3.77	5	-1	1	-3.4	26.04
c.3880G>T	A1294S					6-33447928-G-T			-3.229	Likely Benign	0.089	Likely Benign	Likely Benign	0.276	Likely Benign										-2.21	Neutral	0.997	Probably Damaging	0.991	Probably Damaging	2.19	Pathogenic	0.00	Affected	3.77	5	1	1	-2.6	16.00
c.3881C>A	A1294D					6-33447929-C-A			-4.179	Likely Benign	0.369	Ambiguous	Likely Benign	0.224	Likely Benign										-4.17	Deleterious	0.999	Probably Damaging	0.995	Probably Damaging	2.14	Pathogenic	0.00	Affected	3.77	5	-2	0	-5.3	44.01
c.3881C>T	A1294V					6-33447929-C-T	1	6.45e-7	-3.842	Likely Benign	0.104	Likely Benign	Likely Benign	0.164	Likely Benign										-3.16	Deleterious	0.997	Probably Damaging	0.983	Probably Damaging	2.22	Pathogenic	0.00	Affected	3.77	5	0	0	2.4	28.05
c.3883C>A	Q1295K					6-33447931-C-A			-3.419	Likely Benign	0.343	Ambiguous	Likely Benign	0.313	Likely Benign										-3.30	Deleterious	0.843	Possibly Damaging	0.893	Possibly Damaging	2.38	Pathogenic	0.00	Affected	3.77	5	1	1	-0.4	0.04
c.3884A>G	Q1295R					6-33447932-A-G			-3.342	Likely Benign	0.300	Likely Benign	Likely Benign	0.351	Likely Benign										-3.30	Deleterious	0.925	Possibly Damaging	0.932	Probably Damaging	2.44	Pathogenic	0.00	Affected	3.77	5	1	1	-1.0	28.06
c.3885G>T	Q1295H					6-33447933-G-T			-4.851	Likely Benign	0.588	Likely Pathogenic	Likely Benign	0.349	Likely Benign										-4.08	Deleterious	0.991	Probably Damaging	0.986	Probably Damaging	2.24	Pathogenic	0.00	Affected			3	0	0.3	9.01
c.3889A>G	R1297G					6-33451763-A-G	3	1.86e-6	-2.833	Likely Benign	0.168	Likely Benign	Likely Benign	0.215	Likely Benign										-3.65	Deleterious	0.224	Benign	0.171	Benign	2.56	Benign	0.01	Affected	3.77	5	-2	-3	4.1	-99.14
c.388C>G	Q130E					6-33432685-C-G	2	1.24e-6	-4.283	Likely Benign	0.251	Likely Benign	Likely Benign	0.060	Likely Benign										-0.72	Neutral	0.924	Possibly Damaging	0.857	Possibly Damaging	4.19	Benign	0.08	Tolerated	4.32	2	2	2	0.0	0.98
c.3890G>A	R1297K					6-33451764-G-A	1	6.20e-7	-3.780	Likely Benign	0.114	Likely Benign	Likely Benign	0.074	Likely Benign										0.55	Neutral	0.000	Benign	0.004	Benign	2.80	Benign	1.00	Tolerated	3.77	5	2	3	0.6	-28.01
c.3898C>G	P1300A					6-33451772-C-G	2	1.24e-6	-3.802	Likely Benign	0.073	Likely Benign	Likely Benign	0.065	Likely Benign										0.55	Neutral	0.008	Benign	0.006	Benign	3.23	Benign	1.00	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3898C>T	P1300S					6-33451772-C-T	1	6.20e-7	-3.476	Likely Benign	0.088	Likely Benign	Likely Benign	0.036	Likely Benign										-0.29	Neutral	0.481	Possibly Damaging	0.157	Benign	2.89	Benign	0.27	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3899C>T	P1300L					6-33451773-C-T	1	6.20e-7	-3.562	Likely Benign	0.108	Likely Benign	Likely Benign	0.069	Likely Benign										-1.35	Neutral	0.649	Possibly Damaging	0.209	Benign	2.84	Benign	0.19	Tolerated	3.77	5	-3	-3	5.4	16.04
c.38T>A	I13N					6-33420302-T-A			-3.725	Likely Benign	0.237	Likely Benign	Likely Benign	0.096	Likely Benign										-0.16	Neutral	0.056	Benign	0.005	Benign	4.02	Benign	0.00	Affected	4.32	1	-3	-2	-8.0	0.94
c.38T>C	I13T					6-33420302-T-C			-2.856	Likely Benign	0.385	Ambiguous	Likely Benign	0.132	Likely Benign										-0.02	Neutral	0.024	Benign	0.003	Benign	4.07	Benign	0.00	Affected	4.32	1	-1	0	-5.2	-12.05
c.3901C>A	P1301T					6-33451775-C-A	1	6.20e-7	-4.945	Likely Benign	0.075	Likely Benign	Likely Benign	0.090	Likely Benign										0.34	Neutral	0.000	Benign	0.001	Benign	2.87	Benign	0.47	Tolerated	3.77	5	-1	0	0.9	3.99
c.3901C>G	P1301A					6-33451775-C-G	1	6.20e-7	-4.290	Likely Benign	0.055	Likely Benign	Likely Benign	0.088	Likely Benign										0.66	Neutral	0.003	Benign	0.012	Benign	3.05	Benign	0.88	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3902C>A	P1301H		Conflicting		2	6-33451776-C-A	5	3.10e-6	-5.756	Likely Benign	0.104	Likely Benign	Likely Benign	0.232	Likely Benign										-1.13	Neutral	0.642	Possibly Damaging	0.378	Benign	2.79	Benign	0.04	Affected	3.77	5	0	-2	-1.6	40.02
c.3902C>G	P1301R		Uncertain		1	6-33451776-C-G	15	9.30e-6	-4.753	Likely Benign	0.162	Likely Benign	Likely Benign	0.076	Likely Benign										-1.13	Neutral	0.077	Benign	0.059	Benign	2.81	Benign	0.10	Tolerated	3.77	5	0	-2	-2.9	59.07
c.3902C>T	P1301L					6-33451776-C-T	3	1.86e-6	-4.152	Likely Benign	0.099	Likely Benign	Likely Benign	0.072	Likely Benign										-1.63	Neutral	0.017	Benign	0.028	Benign	2.83	Benign	0.11	Tolerated	3.77	5	-3	-3	5.4	16.04
c.3906G>C	L1302F		Uncertain		1				-5.674	Likely Benign	0.148	Likely Benign	Likely Benign	0.211	Likely Benign										-2.70	Deleterious	0.960	Probably Damaging	0.657	Possibly Damaging	1.53	Pathogenic	0.00	Affected			2	0	-1.0	34.02
c.3907G>A	G1303S		Uncertain		1				-2.271	Likely Benign	0.125	Likely Benign	Likely Benign	0.155	Likely Benign										-0.19	Neutral	0.649	Possibly Damaging	0.433	Benign	2.84	Benign	0.18	Tolerated			1	0	-0.4	30.03
c.3910C>T	P1304S					6-33451784-C-T	1	6.20e-7	-4.103	Likely Benign	0.077	Likely Benign	Likely Benign	0.039	Likely Benign										0.36	Neutral	0.059	Benign	0.041	Benign	3.03	Benign	0.58	Tolerated	3.77	5	-1	1	0.8	-10.04
c.3911C>T	P1304L					6-33451785-C-T	1	6.20e-7	-4.080	Likely Benign	0.100	Likely Benign	Likely Benign	0.137	Likely Benign										-1.33	Neutral	0.126	Benign	0.066	Benign	2.83	Benign	0.06	Tolerated			-3	-3	5.4	16.04
c.3913A>G	T1305A		Conflicting		4	6-33451787-A-G	30	1.86e-5	-2.692	Likely Benign	0.055	Likely Benign	Likely Benign	0.069	Likely Benign										1.74	Neutral	0.000	Benign	0.001	Benign	3.24	Benign	1.00	Tolerated	3.77	5	1	0	2.5	-30.03
c.3917A>C	N1306T					6-33451791-A-C			-1.863	Likely Benign	0.156	Likely Benign	Likely Benign	0.240	Likely Benign										-4.17	Deleterious	0.697	Possibly Damaging	0.399	Benign	2.59	Benign	0.00	Affected	3.77	5	0	0	2.8	-13.00
c.3919C>G	P1307A					6-33451793-C-G	1	6.20e-7	-4.042	Likely Benign	0.078	Likely Benign	Likely Benign	0.064	Likely Benign										0.49	Neutral	0.003	Benign	0.006	Benign	3.11	Benign	1.00	Tolerated	3.77	5	-1	1	3.4	-26.04
c.391G>C	G131R		Uncertain		1				-6.564	Likely Benign	0.983	Likely Pathogenic	Likely Pathogenic	0.099	Likely Benign										-3.82	Deleterious	0.983	Probably Damaging	0.656	Possibly Damaging	3.92	Benign	0.00	Affected	3.61	5	-2	-3	-4.1	99.14
c.3920C>A	P1307Q		Uncertain		1	6-33451794-C-A			-4.227	Likely Benign	0.114	Likely Benign	Likely Benign	0.192	Likely Benign										-0.88	Neutral	0.988	Probably Damaging	0.765	Possibly Damaging	2.82	Benign	0.03	Affected	3.77	5	0	-1	-1.9	31.01
c.3920C>T	P1307L		Uncertain		1	6-33451794-C-T	11	6.82e-6	-4.044	Likely Benign	0.144	Likely Benign	Likely Benign	0.292	Likely Benign										-1.49	Neutral	0.779	Possibly Damaging	0.220	Benign	2.82	Benign	0.04	Affected	3.77	5	-3	-3	5.4	16.04
c.3922C>T	R1308C		Conflicting		2	6-33451796-C-T	4	2.48e-6	-4.994	Likely Benign	0.421	Ambiguous	Likely Benign	0.352	Likely Benign										-4.89	Deleterious	0.999	Probably Damaging	0.993	Probably Damaging	2.31	Pathogenic	0.00	Affected	3.77	5	-4	-3	7.0	-53.05
c.3923G>A	R1308H		Uncertain		1	6-33451797-G-A	3	1.86e-6	-3.586	Likely Benign	0.201	Likely Benign	Likely Benign	0.319	Likely Benign										-3.12	Deleterious	0.998	Probably Damaging	0.991	Probably Damaging	2.33	Pathogenic	0.00	Affected	3.77	5	2	0	1.3	-19.05
c.3923G>C	R1308P					6-33451797-G-C			-1.320	Likely Benign	0.216	Likely Benign	Likely Benign	0.158	Likely Benign										-4.62	Deleterious	0.995	Probably Damaging	0.992	Probably Damaging	2.32	Pathogenic	0.00	Affected	3.77	5	-2	0	2.9	-59.07
c.3925G>A	V1309M					6-33451799-G-A	1	6.20e-7	-4.653	Likely Benign	0.183	Likely Benign	Likely Benign	0.072	Likely Benign										0.18	Neutral	0.651	Possibly Damaging	0.346	Benign	2.44	Pathogenic	0.04	Affected	3.77	5	1	2	-2.3	32.06
c.3929C>T	T1310M		Benign		1	6-33451803-C-T	17	1.05e-5	-4.822	Likely Benign	0.117	Likely Benign	Likely Benign	0.069	Likely Benign										2.19	Neutral	0.021	Benign	0.005	Benign	2.98	Benign	0.93	Tolerated	3.77	5	-1	-1	2.6	30.09
c.3931C>A	L1311M					6-33451805-C-A	3	1.86e-6	-4.817	Likely Benign	0.099	Likely Benign	Likely Benign	0.060	Likely Benign										0.18	Neutral	0.936	Possibly Damaging	0.632	Possibly Damaging	2.73	Benign	0.23	Tolerated	3.77	5	2	4	-1.9	18.03
c.3931C>G	L1311V					6-33451805-C-G	1	6.20e-7	-3.645	Likely Benign	0.066	Likely Benign	Likely Benign	0.025	Likely Benign										-0.05	Neutral	0.362	Benign	0.193	Benign	2.89	Benign	0.32	Tolerated	3.77	5	1	2	0.4	-14.03
c.3932T>C	L1311P		Likely Benign		1	6-33451806-T-C	1	6.21e-7	-1.831	Likely Benign	0.079	Likely Benign	Likely Benign	0.123	Likely Benign										-0.52	Neutral	0.579	Possibly Damaging	0.335	Benign	2.72	Benign	0.18	Tolerated	3.77	5	-3	-3	-5.4	-16.04
c.3934G>T	A1312S					6-33451808-G-T	1	6.21e-7	-3.906	Likely Benign	0.083	Likely Benign	Likely Benign	0.123	Likely Benign										-1.03	Neutral	0.978	Probably Damaging	0.983	Probably Damaging	3.21	Benign	0.00	Affected	3.77	5	1	1	-2.6	16.00
c.3935C>T	A1312V					6-33451809-C-T	4	2.48e-6	-4.585	Likely Benign	0.109	Likely Benign	Likely Benign	0.231	Likely Benign										-1.74	Neutral	0.991	Probably Damaging	0.983	Probably Damaging	3.15	Benign	0.00	Affected	3.77	5	0	0	2.4	28.05
c.3940C>A	P1314T					6-33451814-C-A			-4.083	Likely Benign	0.096	Likely Benign	Likely Benign	0.066	Likely Benign										1.26	Neutral	0.061	Benign	0.045	Benign	4.32	Benign	0.97	Tolerated	3.77	5	-1	0	0.9	3.99
c.3940C>G	P1314A					6-33451814-C-G	1	6.22e-7	-3.540	Likely Benign	0.061	Likely Benign	Likely Benign	0.043	Likely Benign										-0.37	Neutral	0.001	Benign	0.002	Benign	4.23	Benign	0.93	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3941C>A	P1314Q					6-33451815-C-A			-4.222	Likely Benign	0.104	Likely Benign	Likely Benign	0.039	Likely Benign										-0.55	Neutral	0.618	Possibly Damaging	0.333	Benign	4.24	Benign	0.04	Affected	3.77	5	-1	0	-1.9	31.01
c.3941C>T	P1314L		Likely Benign		1	6-33451815-C-T	2	1.24e-6	-4.040	Likely Benign	0.118	Likely Benign	Likely Benign	0.049	Likely Benign										-0.20	Neutral	0.421	Benign	0.066	Benign	4.19	Benign	0.05	Affected	3.77	5	-3	-3	5.4	16.04
c.3943T>C	W1315R		Uncertain		1				0.205	Likely Benign	0.660	Likely Pathogenic	Likely Benign	0.114	Likely Benign										1.31	Neutral	0.000	Benign	0.001	Benign	4.37	Benign	0.91	Tolerated	3.77	5	2	-3	-3.6	-30.03
c.3946A>C	N1316H					6-33451820-A-C			-4.151	Likely Benign	0.246	Likely Benign	Likely Benign	0.069	Likely Benign										-1.87	Neutral	0.939	Possibly Damaging	0.496	Possibly Damaging	3.95	Benign	0.00	Affected	3.77	5	1	2	0.3	23.04
c.3946A>G	N1316D					6-33451820-A-G			-2.717	Likely Benign	0.364	Ambiguous	Likely Benign	0.057	Likely Benign										-2.80	Deleterious	0.225	Benign	0.084	Benign	3.96	Benign	0.00	Affected	3.77	5	1	2	0.0	0.98
c.3946A>T	N1316Y					6-33451820-A-T			-5.579	Likely Benign	0.392	Ambiguous	Likely Benign	0.101	Likely Benign										-2.48	Neutral	0.939	Possibly Damaging	0.396	Benign	3.90	Benign	0.00	Affected	3.77	5	-2	-2	2.2	49.07
c.3947A>C	N1316T					6-33451821-A-C			-3.080	Likely Benign	0.315	Likely Benign	Likely Benign	0.107	Likely Benign										-3.18	Deleterious	0.127	Benign	0.045	Benign	3.96	Benign	0.00	Affected	3.77	5	0	0	2.8	-13.00
c.3947A>G	N1316S					6-33451821-A-G	1	6.25e-7	-2.906	Likely Benign	0.169	Likely Benign	Likely Benign	0.084	Likely Benign										-2.69	Deleterious	0.004	Benign	0.003	Benign	4.03	Benign	0.00	Affected	3.77	5	1	1	2.7	-27.03
c.3948T>A	N1316K					6-33451822-T-A			-3.815	Likely Benign	0.699	Likely Pathogenic	Likely Benign	0.044	Likely Benign										-3.27	Deleterious	0.414	Benign	0.063	Benign	4.00	Benign	0.00	Affected	3.77	5	0	1	-0.4	14.07
c.3948T>G	N1316K					6-33451822-T-G			-3.815	Likely Benign	0.699	Likely Pathogenic	Likely Benign	0.044	Likely Benign										-3.27	Deleterious	0.414	Benign	0.063	Benign	4.00	Benign	0.00	Affected	3.77	5	0	1	-0.4	14.07
c.3949G>A	G1317S		Conflicting		3	6-33451823-G-A	1	6.26e-7	-3.522	Likely Benign	0.145	Likely Benign	Likely Benign	0.092	Likely Benign										-2.45	Neutral	0.127	Benign	0.045	Benign	4.08	Benign	0.00	Affected	3.77	5	1	0	-0.4	30.03
c.3949G>T	G1317C					6-33451823-G-T			-5.850	Likely Benign	0.342	Ambiguous	Likely Benign	0.162	Likely Benign										-3.83	Deleterious	0.939	Possibly Damaging	0.570	Possibly Damaging	3.99	Benign	0.00	Affected	3.77	5	-3	-3	2.9	46.09
c.394T>C	F132L					6-33432691-T-C			-5.401	Likely Benign	0.998	Likely Pathogenic	Likely Pathogenic	0.165	Likely Benign										-2.99	Deleterious	0.000	Benign	0.002	Benign	3.46	Benign	0.00	Affected	3.61	5	0	2	1.0	-34.02
c.3950G>A	G1317D					6-33451824-G-A			-4.860	Likely Benign	0.520	Ambiguous	Likely Benign	0.081	Likely Benign										-3.54	Deleterious	0.588	Possibly Damaging	0.212	Benign	4.03	Benign	0.00	Affected	3.77	5	-1	1	-3.1	58.04
c.3952C>A	L1318M					6-33451826-C-A			-4.625	Likely Benign	0.117	Likely Benign	Likely Benign	0.039	Likely Benign										-0.62	Neutral	0.939	Possibly Damaging	0.396	Benign	4.01	Benign	0.03	Affected	3.77	5	2	4	-1.9	18.03
c.3952C>G	L1318V					6-33451826-C-G	1	6.31e-7	-3.938	Likely Benign	0.091	Likely Benign	Likely Benign	0.038	Likely Benign										-0.58	Neutral	0.113	Benign	0.028	Benign	4.08	Benign	0.75	Tolerated	3.77	5	1	2	0.4	-14.03
c.3953T>A	L1318Q					6-33451827-T-A	1	6.32e-7	-3.445	Likely Benign	0.120	Likely Benign	Likely Benign	0.077	Likely Benign										-2.06	Neutral	0.834	Possibly Damaging	0.307	Benign	4.04	Benign	0.00	Affected	3.77	5	-2	-2	-7.3	14.97
c.3953T>C	L1318P					6-33451827-T-C			-2.307	Likely Benign	0.116	Likely Benign	Likely Benign	0.126	Likely Benign										-2.90	Deleterious	0.813	Possibly Damaging	0.212	Benign	3.98	Benign	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.3953T>G	L1318R					6-33451827-T-G			-3.381	Likely Benign	0.187	Likely Benign	Likely Benign	0.081	Likely Benign										-1.58	Neutral	0.588	Possibly Damaging	0.212	Benign	4.01	Benign	0.01	Affected	3.77	5	-2	-3	-8.3	43.03
c.3955G>A	A1319T					6-33451829-G-A			-4.861	Likely Benign	0.076	Likely Benign	Likely Benign	0.097	Likely Benign										-0.30	Neutral	0.917	Possibly Damaging	0.500	Possibly Damaging	4.13	Benign	0.03	Affected	3.77	5	0	1	-2.5	30.03
c.3955G>C	A1319P					6-33451829-G-C	3	1.95e-6	-2.783	Likely Benign	0.057	Likely Benign	Likely Benign	0.104	Likely Benign										-0.81	Neutral	0.992	Probably Damaging	0.878	Possibly Damaging	4.06	Benign	0.03	Affected	3.77	5	-1	1	-3.4	26.04
c.3955G>T	A1319S					6-33451829-G-T			-4.557	Likely Benign	0.075	Likely Benign	Likely Benign	0.094	Likely Benign										0.79	Neutral	0.174	Benign	0.112	Benign	4.17	Benign	1.00	Tolerated	3.77	5	1	1	-2.6	16.00
c.3956C>A	A1319D					6-33451830-C-A			-5.156	Likely Benign	0.297	Likely Benign	Likely Benign	0.208	Likely Benign										-0.85	Neutral	0.971	Probably Damaging	0.813	Possibly Damaging	4.08	Benign	0.01	Affected	3.77	5	-2	0	-5.3	44.01
c.3956C>G	A1319G		Uncertain		2	6-33451830-C-G			-3.927	Likely Benign	0.084	Likely Benign	Likely Benign	0.128	Likely Benign										-0.74	Neutral	0.819	Possibly Damaging	0.581	Possibly Damaging	4.07	Benign	0.06	Tolerated	3.77	5	1	0	-2.2	-14.03
c.3956C>T	A1319V					6-33451830-C-T	1	7.16e-7	-5.015	Likely Benign	0.082	Likely Benign	Likely Benign	0.167	Likely Benign										-0.17	Neutral	0.971	Probably Damaging	0.757	Possibly Damaging	4.14	Benign	0.02	Affected	3.77	5	0	0	2.4	28.05
c.3958C>A	P1320T					6-33451832-C-A	1	6.42e-7	-5.355	Likely Benign	0.076	Likely Benign	Likely Benign	0.091	Likely Benign										-0.86	Neutral	0.994	Probably Damaging	0.981	Probably Damaging	4.21	Benign	0.00	Affected	3.77	5	-1	0	0.9	3.99
c.3958C>T	P1320S		Uncertain		1	6-33451832-C-T	2	1.28e-6	-4.928	Likely Benign	0.072	Likely Benign	Likely Benign	0.097	Likely Benign										-0.69	Neutral	0.980	Probably Damaging	0.968	Probably Damaging	4.25	Benign	0.00	Affected	3.77	5	1	-1	0.8	-10.04
c.3959C>A	P1320H					6-33451833-C-A	2	1.29e-6	-6.296	Likely Benign	0.136	Likely Benign	Likely Benign	0.114	Likely Benign										-1.05	Neutral	0.998	Probably Damaging	0.990	Probably Damaging	4.17	Benign	0.00	Affected	3.77	5	-2	0	-1.6	40.02
c.3959C>T	P1320L					6-33451833-C-T			-5.187	Likely Benign	0.094	Likely Benign	Likely Benign	0.115	Likely Benign										-1.22	Neutral	0.994	Probably Damaging	0.981	Probably Damaging	4.18	Benign	0.00	Affected	3.77	5	-3	-3	5.4	16.04
c.3961C>A	P1321T					6-33451835-C-A			-4.946	Likely Benign	0.073	Likely Benign	Likely Benign	0.058	Likely Benign										1.07	Neutral	0.115	Benign	0.012	Benign	4.25	Benign	1.00	Tolerated	3.77	5	-1	0	0.9	3.99
c.3961C>G	P1321A					6-33451835-C-G			-4.411	Likely Benign	0.051	Likely Benign	Likely Benign	0.058	Likely Benign										-0.33	Neutral	0.001	Benign	0.000	Benign	4.29	Benign	0.42	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3961C>T	P1321S		Uncertain		1	6-33451835-C-T	10	6.46e-6	-4.897	Likely Benign	0.077	Likely Benign	Likely Benign	0.049	Likely Benign										0.68	Neutral	0.028	Benign	0.004	Benign	4.27	Benign	0.71	Tolerated	3.77	5	1	-1	0.8	-10.04																10.1016/j.ajhg.2020.11.011
c.3962C>A	P1321Q		Benign		1	6-33451836-C-A	1	6.58e-7	-5.594	Likely Benign	0.079	Likely Benign	Likely Benign	0.055	Likely Benign										-0.74	Neutral	0.659	Possibly Damaging	0.034	Benign	4.24	Benign	0.09	Tolerated	3.77	5	0	-1	-1.9	31.01
c.3962C>G	P1321R					6-33451836-C-G	1	6.58e-7	-5.310	Likely Benign	0.154	Likely Benign	Likely Benign	0.034	Likely Benign										-1.10	Neutral	0.389	Benign	0.024	Benign	4.25	Benign	0.09	Tolerated	3.77	5	-2	0	-2.9	59.07
c.3964G>A	A1322T					6-33451838-G-A			-4.940	Likely Benign	0.077	Likely Benign	Likely Benign	0.079	Likely Benign										0.51	Neutral	0.000	Benign	0.000	Benign	4.20	Benign	0.27	Tolerated	3.77	5	0	1	-2.5	30.03
c.3964G>C	A1322P		Benign		1	6-33451838-G-C			-1.153	Likely Benign	0.063	Likely Benign	Likely Benign	0.090	Likely Benign										0.03	Neutral	0.000	Benign	0.000	Benign	4.15	Benign	0.23	Tolerated	3.77	5	1	-1	-3.4	26.04
c.3964G>T	A1322S					6-33451838-G-T			-4.570	Likely Benign	0.073	Likely Benign	Likely Benign	0.086	Likely Benign										1.38	Neutral	0.003	Benign	0.001	Benign	4.48	Benign	0.57	Tolerated	3.77	5	1	1	-2.6	16.00
c.3965C>A	A1322D					6-33451839-C-A			-5.744	Likely Benign	0.284	Likely Benign	Likely Benign	0.092	Likely Benign										0.70	Neutral	0.013	Benign	0.004	Benign	4.17	Benign	0.45	Tolerated	3.77	5	-2	0	-5.3	44.01
c.3965C>G	A1322G					6-33451839-C-G			-4.159	Likely Benign	0.086	Likely Benign	Likely Benign	0.053	Likely Benign										0.42	Neutral	0.005	Benign	0.002	Benign	4.16	Benign	0.62	Tolerated	3.77	5	0	1	-2.2	-14.03
c.3965C>T	A1322V					6-33451839-C-T			-5.376	Likely Benign	0.076	Likely Benign	Likely Benign	0.076	Likely Benign										-0.52	Neutral	0.001	Benign	0.001	Benign	4.17	Benign	0.15	Tolerated	3.77	5	0	0	2.4	28.05
c.3967C>A	P1323T					6-33451841-C-A			-6.296	Likely Benign	0.073	Likely Benign	Likely Benign	0.064	Likely Benign										-0.37	Neutral	0.588	Possibly Damaging	0.227	Benign	3.95	Benign	0.00	Affected	4.32	1	-1	0	0.9	3.99
c.3967C>G	P1323A					6-33451841-C-G			-4.802	Likely Benign	0.053	Likely Benign	Likely Benign	0.040	Likely Benign										-0.73	Neutral	0.011	Benign	0.017	Benign	3.92	Benign	0.00	Affected	4.32	1	-1	1	3.4	-26.04
c.3968C>A	P1323Q					6-33451842-C-A			-6.134	Likely Benign	0.088	Likely Benign	Likely Benign	0.033	Likely Benign										-0.85	Neutral	0.712	Possibly Damaging	0.328	Benign	3.82	Benign	0.00	Affected	4.32	1	-1	0	-1.9	31.01
c.3968C>T	P1323L					6-33451842-C-T	3	1.95e-6	-6.005	Likely Benign	0.084	Likely Benign	Likely Benign	0.045	Likely Benign										-1.04	Neutral	0.414	Benign	0.175	Benign	3.82	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.3970C>A	P1324T					6-33451844-C-A			-5.289	Likely Benign	0.077	Likely Benign	Likely Benign	0.072	Likely Benign										0.95	Neutral	0.588	Possibly Damaging	0.175	Benign	4.43	Benign	0.00	Affected	4.32	1	-1	0	0.9	3.99
c.3970C>T	P1324S		Likely Benign		1	6-33451844-C-T	5	3.26e-6	-5.451	Likely Benign	0.068	Likely Benign	Likely Benign	0.049	Likely Benign										0.35	Neutral	0.225	Benign	0.092	Benign	4.33	Benign	0.00	Affected	4.32	1	1	-1	0.8	-10.04
c.3971C>A	P1324Q					6-33451845-C-A			-5.577	Likely Benign	0.087	Likely Benign	Likely Benign	0.028	Likely Benign										-0.69	Neutral	0.027	Benign	0.010	Benign	4.27	Benign	0.00	Affected	4.32	1	-1	0	-1.9	31.01
c.3971C>T	P1324L					6-33451845-C-T			-5.549	Likely Benign	0.084	Likely Benign	Likely Benign	0.072	Likely Benign										-1.17	Neutral	0.414	Benign	0.175	Benign	4.26	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.3973C>A	P1325T					6-33451847-C-A			-5.880	Likely Benign	0.083	Likely Benign	Likely Benign	0.135	Likely Benign										-0.14	Neutral	0.000	Benign	0.001	Benign	4.07	Benign	0.00	Affected	4.32	1	-1	0	0.9	3.99
c.3973C>G	P1325A					6-33451847-C-G			-3.786	Likely Benign	0.058	Likely Benign	Likely Benign	0.083	Likely Benign										-0.95	Neutral	0.019	Benign	0.004	Benign	4.10	Benign	0.00	Affected	4.32	1	-1	1	3.4	-26.04
c.3973C>T	P1325S					6-33451847-C-T	1	6.43e-7	-5.273	Likely Benign	0.083	Likely Benign	Likely Benign	0.053	Likely Benign										0.29	Neutral	0.010	Benign	0.007	Benign	4.10	Benign	0.00	Affected	4.32	1	-1	1	0.8	-10.04
c.3974C>A	P1325H					6-33451848-C-A			-6.970	Likely Benign	0.136	Likely Benign	Likely Benign	0.056	Likely Benign										0.10	Neutral	0.704	Possibly Damaging	0.187	Benign	4.04	Benign	0.00	Affected	4.32	1	-2	0	-1.6	40.02
c.3974C>T	P1325L		Uncertain		1	6-33451848-C-T			-5.256	Likely Benign	0.085	Likely Benign	Likely Benign	0.146	Likely Benign										-1.05	Neutral	0.000	Benign	0.000	Benign	4.05	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.3976C>A	P1326T					6-33451850-C-A			-5.755	Likely Benign	0.117	Likely Benign	Likely Benign	0.135	Likely Benign										-0.26	Neutral	0.999	Probably Damaging	0.992	Probably Damaging	3.71	Benign	0.00	Affected	3.77	5	-1	0	0.9	3.99
c.3976C>T	P1326S					6-33451850-C-T			-5.221	Likely Benign	0.121	Likely Benign	Likely Benign	0.107	Likely Benign										-0.35	Neutral	0.999	Probably Damaging	0.992	Probably Damaging	3.74	Benign	0.00	Affected	3.77	5	-1	1	0.8	-10.04
c.3977C>A	P1326Q		Uncertain		1	6-33451851-C-A	1	6.40e-7	-5.422	Likely Benign	0.128	Likely Benign	Likely Benign	0.138	Likely Benign										-0.86	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	3.62	Benign	0.00	Affected	3.77	5	-1	0	-1.9	31.01
c.3977C>G	P1326R		Uncertain		1				-5.097	Likely Benign	0.240	Likely Benign	Likely Benign	0.133	Likely Benign										-0.82	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	3.62	Benign	0.00	Affected	3.77	5	0	-2	-2.9	59.07
c.3977C>T	P1326L		Uncertain		1				-5.541	Likely Benign	0.115	Likely Benign	Likely Benign	0.117	Likely Benign										-1.06	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	3.62	Benign	0.00	Affected	3.77	5	-3	-3	5.4	16.04
c.3979C>A	P1327T					6-33451853-C-A			-5.263	Likely Benign	0.150	Likely Benign	Likely Benign	0.144	Likely Benign										1.20	Neutral	0.994	Probably Damaging	0.908	Possibly Damaging	4.51	Benign	1.00	Tolerated	3.77	5	-1	0	0.9	3.99
c.3979C>G	P1327A					6-33451853-C-G	2	1.28e-6	-4.661	Likely Benign	0.089	Likely Benign	Likely Benign	0.072	Likely Benign										-0.37	Neutral	0.980	Probably Damaging	0.811	Possibly Damaging	4.24	Benign	0.42	Tolerated	3.77	5	-1	1	3.4	-26.04
c.3979C>T	P1327S		Uncertain		1	6-33451853-C-T			-4.744	Likely Benign	0.131	Likely Benign	Likely Benign	0.092	Likely Benign										0.28	Neutral	0.980	Probably Damaging	0.857	Possibly Damaging	4.25	Benign	0.71	Tolerated	3.77	5	1	-1	0.8	-10.04
c.3980C>A	P1327H					6-33451854-C-A			-5.496	Likely Benign	0.263	Likely Benign	Likely Benign	0.144	Likely Benign										-0.49	Neutral	0.998	Probably Damaging	0.953	Probably Damaging	4.09	Benign	0.04	Affected	3.77	5	-2	0	-1.6	40.02
c.3980C>G	P1327R					6-33451854-C-G			-4.724	Likely Benign	0.273	Likely Benign	Likely Benign	0.137	Likely Benign										-0.95	Neutral	0.994	Probably Damaging	0.937	Probably Damaging	4.12	Benign	0.09	Tolerated	3.77	5	-2	0	-2.9	59.07
c.3980C>T	P1327L		Uncertain		1	6-33451854-C-T	2	1.28e-6	-5.264	Likely Benign	0.242	Likely Benign	Likely Benign	0.142	Likely Benign										-1.24	Neutral	0.994	Probably Damaging	0.908	Possibly Damaging	4.12	Benign	0.10	Tolerated	3.77	5	-3	-3	5.4	16.04
c.3982C>T	R1328W					6-33451856-C-T	4	2.56e-6	-7.022	In-Between	0.779	Likely Pathogenic	Likely Benign	0.125	Likely Benign										-2.40	Neutral	0.997	Probably Damaging	0.756	Possibly Damaging	4.04	Benign	0.00	Affected	3.77	5	-3	2	3.6	30.03
c.3983G>A	R1328Q		Uncertain		3	6-33451857-G-A	35	1.49e-4	-2.921	Likely Benign	0.273	Likely Benign	Likely Benign	0.043	Likely Benign										-1.02	Neutral	0.799	Possibly Damaging	0.098	Benign	4.12	Benign	0.03	Affected	3.77	5	1	1	1.0	-28.06
c.3983G>C	R1328P		Benign		1	6-33451857-G-C			-1.220	Likely Benign	0.466	Ambiguous	Likely Benign	0.060	Likely Benign										-2.01	Neutral	0.927	Possibly Damaging	0.452	Possibly Damaging	4.06	Benign	0.01	Affected	3.77	5	0	-2	2.9	-59.07
c.3983G>T	R1328L					6-33451857-G-T			-3.233	Likely Benign	0.452	Ambiguous	Likely Benign	0.038	Likely Benign										-1.94	Neutral	0.784	Possibly Damaging	0.145	Benign	4.08	Benign	0.01	Affected	3.77	5	-2	-3	8.3	-43.03
c.3985C>A	L1329M					6-33451859-C-A			-5.493	Likely Benign	0.780	Likely Pathogenic	Likely Benign	0.087	Likely Benign										-1.16	Neutral	0.994	Probably Damaging	0.990	Probably Damaging	3.10	Benign	0.00	Affected	3.77	5	2	4	-1.9	18.03
c.3985C>G	L1329V					6-33451859-C-G	1	6.40e-7	-4.209	Likely Benign	0.770	Likely Pathogenic	Likely Benign	0.077	Likely Benign										-1.55	Neutral	0.980	Probably Damaging	0.952	Probably Damaging	3.18	Benign	0.00	Affected	3.77	5	1	2	0.4	-14.03
c.3986T>A	L1329Q					6-33451860-T-A			-4.106	Likely Benign	0.956	Likely Pathogenic	Likely Pathogenic	0.157	Likely Benign										-3.31	Deleterious	0.994	Probably Damaging	0.993	Probably Damaging	3.05	Benign	0.00	Affected	3.77	5	-2	-2	-7.3	14.97
c.3986T>C	L1329P					6-33451860-T-C			-2.903	Likely Benign	0.951	Likely Pathogenic	Ambiguous	0.165	Likely Benign										-3.74	Deleterious	0.994	Probably Damaging	0.993	Probably Damaging	3.04	Benign	0.00	Affected	3.77	5	-3	-3	-5.4	-16.04
c.3986T>G	L1329R					6-33451860-T-G			-3.636	Likely Benign	0.923	Likely Pathogenic	Ambiguous	0.141	Likely Benign										-3.16	Deleterious	0.994	Probably Damaging	0.990	Probably Damaging	3.05	Benign	0.00	Affected	3.77	5	-2	-3	-8.3	43.03
c.3988C>A	Q1330K					6-33451862-C-A			-4.120	Likely Benign	0.605	Likely Pathogenic	Likely Benign	0.027	Likely Benign										-1.52	Neutral	0.544	Possibly Damaging	0.259	Benign	3.98	Benign	0.04	Affected	3.77	5	1	1	-0.4	0.04
c.3989A>C	Q1330P					6-33451863-A-C			-3.087	Likely Benign	0.814	Likely Pathogenic	Ambiguous	0.076	Likely Benign										-2.45	Neutral	0.898	Possibly Damaging	0.441	Benign	3.91	Benign	0.03	Affected	3.77	5	-1	0	1.9	-31.01
c.3989A>G	Q1330R					6-33451863-A-G			-3.601	Likely Benign	0.472	Ambiguous	Likely Benign	0.031	Likely Benign										-1.65	Neutral	0.898	Possibly Damaging	0.341	Benign	3.95	Benign	0.03	Affected	3.77	5	1	1	-1.0	28.06
c.3992T>A	I1331N					6-33451866-T-A			-3.788	Likely Benign	0.994	Likely Pathogenic	Likely Pathogenic	0.237	Likely Benign										-4.09	Deleterious	0.984	Probably Damaging	0.979	Probably Damaging	3.29	Benign	0.00	Affected	3.77	5	-3	-2	-8.0	0.94
c.3994A>T	T1332S					6-33451868-A-T			-3.085	Likely Benign	0.674	Likely Pathogenic	Likely Benign	0.163	Likely Benign										-2.29	Neutral	0.980	Probably Damaging	0.935	Probably Damaging	3.00	Benign	0.00	Affected	3.77	5	1	1	-0.1	-14.03
c.3995C>A	T1332K					6-33451869-C-A			-3.264	Likely Benign	0.935	Likely Pathogenic	Ambiguous	0.247	Likely Benign										-3.48	Deleterious	0.998	Probably Damaging	0.989	Probably Damaging	2.96	Benign	0.00	Affected	3.77	5	-1	0	-3.2	27.07
c.3995C>T	T1332M		Likely Benign		1	6-33451869-C-T	20	1.86e-5	-4.107	Likely Benign	0.948	Likely Pathogenic	Ambiguous	0.252	Likely Benign										-3.63	Deleterious	1.000	Probably Damaging	0.991	Probably Damaging	2.95	Benign	0.00	Affected	3.77	5	-1	-1	2.6	30.09
c.39C>G	I13M					6-33420303-C-G	1	6.49e-7	-4.097	Likely Benign	0.170	Likely Benign	Likely Benign	0.093	Likely Benign										0.16	Neutral	0.296	Benign	0.022	Benign	4.04	Benign	0.00	Affected	4.32	1	1	2	-2.6	18.03
c.3G>A	M1I		Conflicting		3				-5.397	Likely Benign				0.227	Likely Benign										-0.17	Neutral	0.001	Benign	0.000	Benign	4.25	Benign	0.00	Affected	4.32	1	2	1	2.6	-18.03
c.4000A>G	N1334D					6-33451874-A-G			-4.584	Likely Benign	0.674	Likely Pathogenic	Likely Benign	0.126	Likely Benign										-3.06	Deleterious	0.886	Possibly Damaging	0.522	Possibly Damaging	3.55	Benign	0.00	Affected	3.77	5	1	2	0.0	0.98
c.4002C>A	N1334K					6-33451876-C-A			-4.875	Likely Benign	0.933	Likely Pathogenic	Ambiguous	0.109	Likely Benign										-3.49	Deleterious	0.979	Probably Damaging	0.756	Possibly Damaging	3.54	Benign	0.00	Affected	3.77	5	0	1	-0.4	14.07
c.4003G>A	G1335S		Conflicting		2	6-33451877-G-A	3	2.37e-6	-4.495	Likely Benign	0.986	Likely Pathogenic	Likely Pathogenic	0.362	Likely Benign										-3.79	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	2.04	Pathogenic	0.00	Affected	3.77	5	1	0	-0.4	30.03
c.4003G>T	G1335C					6-33451877-G-T	1	7.91e-7	-6.878	Likely Benign	0.997	Likely Pathogenic	Likely Pathogenic	0.426	Likely Benign										-5.51	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.01	Pathogenic	0.00	Affected	3.77	5	-3	-3	2.9	46.09
c.4004G>A	G1335D					6-33451878-G-A			-5.687	Likely Benign	0.998	Likely Pathogenic	Likely Pathogenic	0.404	Likely Benign										-4.42	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	2.02	Pathogenic	0.00	Affected	3.77	5	-1	1	-3.1	58.04
c.4006G>A	E1336K		Benign		2	6-33451880-G-A	6	4.20e-6	-4.697	Likely Benign	0.977	Likely Pathogenic	Likely Pathogenic	0.272	Likely Benign										-2.44	Neutral	0.748	Possibly Damaging	0.079	Benign	3.23	Benign	0.00	Affected	3.77	5	0	1	-0.4	-0.94
c.4008G>C	E1336D		Likely Benign		1				-3.344	Likely Benign	0.596	Likely Pathogenic	Likely Benign	0.062	Likely Benign										-1.92	Neutral	0.001	Benign	0.003	Benign	3.30	Benign	0.00	Affected	3.77	5	2	3	0.0	-14.03
c.4008G>T	E1336D					6-33451882-G-T			-3.344	Likely Benign	0.596	Likely Pathogenic	Likely Benign	0.065	Likely Benign										-1.92	Neutral	0.001	Benign	0.003	Benign	3.30	Benign	0.00	Affected	3.77	5	2	3	0.0	-14.03
c.4011C>A	F1337L					6-33451885-C-A			-2.396	Likely Benign	0.999	Likely Pathogenic	Likely Pathogenic	0.111	Likely Benign										-3.17	Deleterious	0.880	Possibly Damaging	0.899	Possibly Damaging	2.81	Benign	0.00	Affected	3.77	5	0	2	1.0	-34.02
c.4013G>A	R1338Q		Conflicting		3	6-33451887-G-A	12	8.40e-6	-3.494	Likely Benign	0.317	Likely Benign	Likely Benign	0.076	Likely Benign										-1.87	Neutral	0.896	Possibly Damaging	0.194	Benign	3.81	Benign	0.02	Affected	3.77	5	1	1	1.0	-28.06
c.4013G>T	R1338L					6-33451887-G-T			-3.359	Likely Benign	0.587	Likely Pathogenic	Likely Benign	0.232	Likely Benign										-3.65	Deleterious	0.001	Benign	0.001	Benign	3.78	Benign	0.01	Affected	3.77	5	-2	-3	8.3	-43.03
c.4015A>G	N1339D					6-33451889-A-G			-2.533	Likely Benign	0.634	Likely Pathogenic	Likely Benign	0.186	Likely Benign										-3.04	Deleterious	0.980	Probably Damaging	0.956	Probably Damaging	2.92	Benign	0.00	Affected	3.77	5	1	2	0.0	0.98
c.4017C>A	N1339K					6-33451891-C-A			-3.009	Likely Benign	0.872	Likely Pathogenic	Ambiguous	0.169	Likely Benign										-3.56	Deleterious	0.980	Probably Damaging	0.968	Probably Damaging	2.90	Benign	0.00	Affected	3.77	5	0	1	-0.4	14.07
c.4018A>C	T1340P					6-33451892-A-C			-2.681	Likely Benign	0.102	Likely Benign	Likely Benign	0.190	Likely Benign										-1.81	Neutral	0.334	Benign	0.099	Benign	4.08	Benign	0.01	Affected	3.77	5	-1	0	-0.9	-3.99
c.4019C>A	T1340N					6-33451893-C-A			-3.664	Likely Benign	0.154	Likely Benign	Likely Benign	0.071	Likely Benign										-0.95	Neutral	0.092	Benign	0.026	Benign	4.09	Benign	0.02	Affected	3.77	5	0	0	-2.8	13.00
c.4019C>T	T1340I					6-33451893-C-T			-3.476	Likely Benign	0.402	Ambiguous	Likely Benign	0.089	Likely Benign										-2.57	Deleterious	0.334	Benign	0.099	Benign	4.08	Benign	0.01	Affected	3.77	5	-1	0	5.2	12.05
c.401G>A	S134N		Uncertain		1				-5.534	Likely Benign	0.813	Likely Pathogenic	Ambiguous	0.075	Likely Benign										-1.62	Neutral	0.001	Benign	0.002	Benign	3.90	Benign	0.00	Affected	3.61	5	1	1	-2.7	27.03
c.401G>C	S134T					6-33432698-G-C	1	6.32e-7	-5.187	Likely Benign	0.563	Ambiguous	Likely Benign	0.069	Likely Benign										-1.76	Neutral	0.034	Benign	0.047	Benign	3.85	Benign	0.00	Affected	3.61	5	1	1	0.1	14.03
c.4021G>A	A1341T		Uncertain		3	6-33451895-G-A	45	3.44e-5	-3.224	Likely Benign	0.081	Likely Benign	Likely Benign	0.099	Likely Benign										-0.58	Neutral	0.000	Benign	0.000	Benign	4.09	Benign	0.03	Affected	3.77	5	1	0	-2.5	30.03
c.4021G>T	A1341S		Uncertain		1	6-33451895-G-T			-2.867	Likely Benign	0.077	Likely Benign	Likely Benign	0.099	Likely Benign										0.80	Neutral	0.000	Benign	0.001	Benign	4.40	Benign	1.00	Tolerated	3.77	5	1	1	-2.6	16.00
c.4022C>T	A1341V					6-33451896-C-T	1	6.29e-7	-3.687	Likely Benign	0.131	Likely Benign	Likely Benign	0.066	Likely Benign										-1.90	Neutral	0.006	Benign	0.011	Benign	4.04	Benign	0.02	Affected	3.77	5	0	0	2.4	28.05
c.4024G>A	D1342N					6-33451898-G-A			-3.459	Likely Benign	0.140	Likely Benign	Likely Benign	0.058	Likely Benign										0.29	Neutral	0.000	Benign	0.002	Benign	4.07	Benign	0.93	Tolerated	4.32	4	1	2	0.0	-0.98
c.4024G>T	D1342Y					6-33451898-G-T			-4.108	Likely Benign	0.398	Ambiguous	Likely Benign	0.095	Likely Benign										-1.34	Neutral	0.939	Possibly Damaging	0.496	Possibly Damaging	3.98	Benign	0.01	Affected	4.32	4	-3	-4	2.2	48.09
c.4025A>G	D1342G					6-33451899-A-G	1	7.29e-7	-3.227	Likely Benign	0.129	Likely Benign	Likely Benign	0.021	Likely Benign										-0.89	Neutral	0.225	Benign	0.045	Benign	4.05	Benign	0.09	Tolerated	4.32	4	-1	1	3.1	-58.04
c.4026C>A	D1342E					6-33451900-C-A			-3.169	Likely Benign	0.134	Likely Benign	Likely Benign	0.026	Likely Benign										-0.88	Neutral	0.225	Benign	0.084	Benign	4.16	Benign	0.04	Affected	4.32	4	2	3	0.0	14.03
c.4027C>T	H1343Y					6-33451901-C-T			-3.479	Likely Benign	0.139	Likely Benign	Likely Benign	0.040	Likely Benign										-0.85	Neutral	0.444	Benign	0.071	Benign	4.06	Benign	0.00	Affected	4.32	1	2	0	1.9	26.03
c.4028A>T	H1343L					6-33451902-A-T			-1.552	Likely Benign	0.132	Likely Benign	Likely Benign	0.058	Likely Benign										-1.28	Neutral	0.053	Benign	0.012	Benign	4.07	Benign	0.00	Affected	4.32	1	-3	-2	7.0	-23.98
c.4029C>A	H1343Q					6-33451903-C-A			-2.900	Likely Benign	0.111	Likely Benign	Likely Benign	0.035	Likely Benign										-1.04	Neutral	0.659	Possibly Damaging	0.104	Benign	4.06	Benign	0.00	Affected	4.32	1	0	3	-0.3	-9.01
c.404G>A	R135Q		Uncertain		1	6-33432701-G-A	5	3.84e-6	-8.011	Likely Pathogenic	0.853	Likely Pathogenic	Ambiguous	0.087	Likely Benign										-1.94	Neutral	0.327	Benign	0.100	Benign	3.76	Benign	0.02	Affected	3.61	5	1	1	1.0	-28.06
c.406C>T	R136W		Uncertain		2				-10.453	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.237	Likely Benign										-4.71	Deleterious	0.965	Probably Damaging	0.416	Benign	3.45	Benign	0.00	Affected	3.61	5	2	-3	3.6	30.03
c.407G>A	R136Q		Uncertain		1	6-33432704-G-A	13	9.17e-6	-11.146	Likely Pathogenic	0.950	Likely Pathogenic	Ambiguous	0.190	Likely Benign										-2.26	Neutral	0.957	Probably Damaging	0.342	Benign	3.52	Benign	0.01	Affected	3.61	5	1	1	1.0	-28.06
c.407G>C	R136P		Uncertain		1				-11.952	Likely Pathogenic	0.981	Likely Pathogenic	Likely Pathogenic	0.277	Likely Benign										-3.72	Deleterious	0.910	Possibly Damaging	0.578	Possibly Damaging	3.47	Benign	0.00	Affected	3.61	5	0	-2	2.9	-59.07
c.407G>T	R136L					6-33432704-G-T	1	7.05e-7	-11.512	Likely Pathogenic	0.987	Likely Pathogenic	Likely Pathogenic	0.347	Likely Benign										-4.19	Deleterious	0.190	Benign	0.037	Benign	3.48	Benign	0.01	Affected	3.61	5	-2	-3	8.3	-43.03
c.40C>A	P14T					6-33420304-C-A			-3.261	Likely Benign	0.149	Likely Benign	Likely Benign	0.078	Likely Benign										-0.27	Neutral	0.212	Benign	0.014	Benign	4.20	Benign	0.00	Affected	4.32	1	-1	0	0.9	3.99
c.416G>A	S139N		Uncertain		1	6-33432713-G-A	3	2.22e-6	-4.584	Likely Benign	0.688	Likely Pathogenic	Likely Benign	0.109	Likely Benign										-0.75	Neutral	0.149	Benign	0.047	Benign	4.14	Benign	0.24	Tolerated	3.61	5	1	1	-2.7	27.03
c.41C>A	P14H					6-33420305-C-A			-3.747	Likely Benign	0.231	Likely Benign	Likely Benign	0.171	Likely Benign										-0.27	Neutral	0.742	Possibly Damaging	0.091	Benign	4.15	Benign	0.00	Affected	4.32	1	-2	0	-1.6	40.02
c.41C>T	P14L					6-33420305-C-T			-3.277	Likely Benign	0.332	Likely Benign	Likely Benign	0.153	Likely Benign										-0.53	Neutral	0.062	Benign	0.004	Benign	4.19	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.421A>G	I141V					6-33432718-A-G	1	6.42e-7	-4.030	Likely Benign	0.785	Likely Pathogenic	Ambiguous	0.125	Likely Benign										-0.58	Neutral	0.016	Benign	0.021	Benign	3.74	Benign	0.03	Affected	3.61	5	3	4	-0.3	-14.03
c.428G>A	R143Q					6-33432725-G-A	2	1.35e-6	-12.110	Likely Pathogenic	0.988	Likely Pathogenic	Likely Pathogenic	0.181	Likely Benign										-2.48	Neutral	0.678	Possibly Damaging	0.176	Benign	3.53	Benign	0.00	Affected	3.61	5	1	1	1.0	-28.06
c.428G>C	R143P					6-33432725-G-C	2	1.35e-6	-14.564	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.292	Likely Benign										-3.74	Deleterious	0.001	Benign	0.000	Benign	3.49	Benign	0.00	Affected	3.61	5	-2	0	2.9	-59.07
c.428G>T	R143L					6-33432725-G-T	1	6.77e-7	-14.250	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.316	Likely Benign										-4.37	Deleterious	0.319	Benign	0.124	Benign	3.52	Benign	0.00	Affected	3.61	5	-2	-3	8.3	-43.03
c.431C>T	T144M		Uncertain		2	6-33432728-C-T	2	1.30e-6	-11.228	Likely Pathogenic	0.922	Likely Pathogenic	Ambiguous	0.118	Likely Benign										-3.16	Deleterious	0.913	Possibly Damaging	0.333	Benign	3.73	Benign	0.00	Affected	3.61	5	-1	-1	2.6	30.09
c.434A>G	K145R					6-33432731-A-G	1	6.20e-7	-7.685	In-Between	0.213	Likely Benign	Likely Benign	0.128	Likely Benign										-1.58	Neutral	0.399	Benign	0.212	Benign	3.71	Benign	0.00	Affected	3.61	5	2	3	-0.6	28.01
c.43G>A	A15T		Uncertain		1	6-33420307-G-A	4	2.60e-6	-3.720	Likely Benign	0.125	Likely Benign	Likely Benign	0.086	Likely Benign										-0.08	Neutral	0.602	Possibly Damaging	0.017	Benign	4.16	Benign	0.00	Affected	4.32	1	1	0	-2.5	30.03
c.43G>T	A15S					6-33420307-G-T			-2.925	Likely Benign	0.084	Likely Benign	Likely Benign	0.074	Likely Benign										0.11	Neutral	0.122	Benign	0.010	Benign	4.17	Benign	0.00	Affected	4.32	1	1	1	-2.6	16.00
c.442C>G	P148A					6-33432739-C-G	1	6.33e-7	-6.890	Likely Benign	0.729	Likely Pathogenic	Likely Benign	0.117	Likely Benign										-2.31	Neutral	0.999	Probably Damaging	0.991	Probably Damaging	4.00	Benign	0.03	Affected	3.61	5	-1	1	3.4	-26.04
c.442C>T	P148S					6-33432739-C-T	1	6.33e-7	-3.258	Likely Benign	0.874	Likely Pathogenic	Ambiguous	0.102	Likely Benign										-1.81	Neutral	1.000	Probably Damaging	0.994	Probably Damaging	4.05	Benign	0.39	Tolerated	3.61	5	-1	1	0.8	-10.04
c.44C>A	A15E					6-33420308-C-A			-3.423	Likely Benign	0.277	Likely Benign	Likely Benign	0.169	Likely Benign										0.46	Neutral	0.406	Benign	0.040	Benign	4.13	Benign	0.00	Affected	4.32	1	-1	0	-5.3	58.04
c.44C>G	A15G					6-33420308-C-G	3	1.95e-6	-3.261	Likely Benign	0.104	Likely Benign	Likely Benign	0.084	Likely Benign										-0.04	Neutral	0.000	Benign	0.000	Benign	4.12	Benign	0.00	Affected	4.32	1	0	1	-2.2	-14.03
c.44C>T	A15V		Uncertain		1	6-33420308-C-T	1	6.49e-7	-3.560	Likely Benign	0.161	Likely Benign	Likely Benign	0.105	Likely Benign										0.20	Neutral	0.602	Possibly Damaging	0.015	Benign	4.19	Benign	0.00	Affected	4.32	1	0	0	2.4	28.05
c.451G>C	D151H		Uncertain		1	6-33432748-G-C	2	1.26e-6	-11.747	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.335	Likely Benign										-3.90	Deleterious	0.999	Probably Damaging	0.995	Probably Damaging	3.86	Benign	0.00	Affected	3.61	5	-1	1	0.3	22.05
c.452A>C	D151A					6-33432749-A-C	1	6.21e-7	-9.693	Likely Pathogenic	0.986	Likely Pathogenic	Likely Pathogenic	0.326	Likely Benign										-4.51	Deleterious	0.998	Probably Damaging	0.991	Probably Damaging	3.91	Benign	0.01	Affected	3.61	5	-2	0	5.3	-44.01
c.453C>A	D151E		Uncertain		1				-5.662	Likely Benign	0.886	Likely Pathogenic	Ambiguous	0.142	Likely Benign										-2.02	Neutral	0.984	Probably Damaging	0.967	Probably Damaging	3.99	Benign	0.11	Tolerated	3.61	5	3	2	0.0	14.03
c.455G>A	R152Q					6-33432752-G-A	5	3.14e-6	-10.336	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.181	Likely Benign										-2.34	Neutral	0.997	Probably Damaging	0.968	Probably Damaging	3.89	Benign	0.00	Affected	3.61	5	1	1	1.0	-28.06
c.458C>A	T153N		Conflicting		3				-0.739	Likely Benign	0.226	Likely Benign	Likely Benign	0.161	Likely Benign										0.88	Neutral	0.888	Possibly Damaging	0.537	Possibly Damaging	4.23	Benign	0.81	Tolerated	3.61	5	0	0	-2.8	13.00
c.469C>T	R157C					6-33432766-C-T	7	4.34e-6	-11.524	Likely Pathogenic	0.880	Likely Pathogenic	Ambiguous	0.237	Likely Benign										-4.02	Deleterious	1.000	Probably Damaging	0.990	Probably Damaging	3.77	Benign	0.00	Affected	3.74	4	-3	-4	7.0	-53.05
c.46A>G	M16V					6-33420310-A-G	16	1.05e-5	-1.595	Likely Benign	0.128	Likely Benign	Likely Benign	0.073	Likely Benign										-0.07	Neutral	0.000	Benign	0.000	Benign	4.30	Benign	0.00	Affected	4.32	1	1	2	2.3	-32.06
c.470G>A	R157H		Uncertain		1	6-33432767-G-A	1	6.20e-7	-10.235	Likely Pathogenic	0.604	Likely Pathogenic	Likely Benign	0.254	Likely Benign										-2.23	Neutral	0.999	Probably Damaging	0.987	Probably Damaging	3.80	Benign	0.00	Affected	3.74	4	2	0	1.3	-19.05
c.484C>G	R162G		Uncertain		1				-6.985	Likely Benign	0.664	Likely Pathogenic	Likely Benign	0.190	Likely Benign										-0.73	Neutral	0.487	Possibly Damaging	0.272	Benign	4.09	Benign	0.78	Tolerated	3.74	4	-2	-3	4.1	-99.14
c.484C>T	R162C		Pathogenic		2				-8.157	Likely Pathogenic	0.787	Likely Pathogenic	Ambiguous	0.150	Likely Benign										-2.05	Neutral	0.988	Probably Damaging	0.513	Possibly Damaging	4.00	Benign	0.11	Tolerated	3.74	4	-4	-3	7.0	-53.05
c.485G>A	R162H		Uncertain		1	6-33432782-G-A	2	1.24e-6	-9.730	Likely Pathogenic	0.480	Ambiguous	Likely Benign	0.167	Likely Benign										-1.13	Neutral	0.957	Probably Damaging	0.513	Possibly Damaging	4.03	Benign	0.12	Tolerated	3.74	4	2	0	1.3	-19.05
c.48G>A	M16I		Uncertain		1	6-33420312-G-A	1	6.49e-7	-2.198	Likely Benign	0.722	Likely Pathogenic	Likely Benign	0.057	Likely Benign										-0.15	Neutral	0.000	Benign	0.000	Benign	4.28	Benign	0.00	Affected	4.32	1	2	1	2.6	-18.03
c.48G>T	M16I					6-33420312-G-T			-2.198	Likely Benign	0.722	Likely Pathogenic	Likely Benign	0.057	Likely Benign										-0.15	Neutral	0.000	Benign	0.000	Benign	4.28	Benign	0.00	Affected	4.32	1	2	1	2.6	-18.03
c.491G>A	R164Q		Uncertain		1	6-33432788-G-A	2	1.24e-6	-11.208	Likely Pathogenic	0.600	Likely Pathogenic	Likely Benign	0.184	Likely Benign										-1.86	Neutral	0.957	Probably Damaging	0.342	Benign	3.82	Benign	0.00	Affected	3.74	4	1	1	1.0	-28.06
c.491G>C	R164P					6-33432788-G-C	1	6.20e-7	-12.792	Likely Pathogenic	0.897	Likely Pathogenic	Ambiguous	0.339	Likely Benign										-3.42	Deleterious	0.910	Possibly Damaging	0.578	Possibly Damaging	3.77	Benign	0.00	Affected	3.74	4	-2	0	2.9	-59.07
c.499G>A	D167N					6-33432796-G-A	3	1.86e-6	-11.939	Likely Pathogenic	0.843	Likely Pathogenic	Ambiguous	0.097	Likely Benign										-2.32	Neutral	0.141	Benign	0.123	Benign	3.96	Benign	0.00	Affected	3.74	4	1	2	0.0	-0.98
c.4A>G	S2G					6-33420268-A-G	1	6.58e-7	-4.273	Likely Benign	0.124	Likely Benign	Likely Benign	0.079	Likely Benign										-0.48	Neutral	0.012	Benign	0.002	Benign	4.10	Benign	0.00	Affected	4.32	1	0	1	0.4	-30.03
c.502C>T	H168Y		Benign		1				-8.914	Likely Pathogenic	0.264	Likely Benign	Likely Benign	0.065	Likely Benign										-1.53	Neutral	0.192	Benign	0.062	Benign	4.18	Benign	0.01	Affected	4.32	3	0	2	1.9	26.03
c.503A>G	H168R					6-33432800-A-G	1	6.20e-7	-7.334	In-Between	0.395	Ambiguous	Likely Benign	0.153	Likely Benign										-1.08	Neutral	0.016	Benign	0.011	Benign	4.26	Benign	0.02	Affected	4.32	3	0	2	-1.3	19.05
c.505G>A	D169N		Uncertain		1				-10.713	Likely Pathogenic	0.761	Likely Pathogenic	Likely Benign	0.110	Likely Benign										-2.04	Neutral	0.079	Benign	0.052	Benign	4.07	Benign	0.01	Affected	3.74	4	2	1	0.0	-0.98
c.508C>T	R170W		Uncertain		1				-11.660	Likely Pathogenic	0.978	Likely Pathogenic	Likely Pathogenic	0.241	Likely Benign										-4.28	Deleterious	0.999	Probably Damaging	0.849	Possibly Damaging	3.84	Benign	0.00	Affected	3.74	4	2	-3	3.6	30.03
c.509G>A	R170Q		Pathogenic/Likely path.		5				-9.021	Likely Pathogenic	0.798	Likely Pathogenic	Ambiguous	0.221	Likely Benign										-2.31	Neutral	0.947	Possibly Damaging	0.342	Benign	3.91	Benign	0.00	Affected	3.74	4	1	1	1.0	-28.06																10.1016/j.ajhg.2020.11.011
c.50C>A	S17Y					6-33420314-C-A			-4.492	Likely Benign	0.551	Ambiguous	Likely Benign	0.050	Likely Benign										-1.06	Neutral	0.742	Possibly Damaging	0.047	Benign	3.99	Benign	0.00	Affected	4.32	1	-2	-3	-0.5	76.10
c.50C>T	S17F		Uncertain		1	6-33420314-C-T	10	6.49e-6	-3.888	Likely Benign	0.637	Likely Pathogenic	Likely Benign	0.048	Likely Benign										-0.99	Neutral	0.486	Possibly Damaging	0.032	Benign	3.99	Benign	0.00	Affected	4.32	1	-2	-3	3.6	60.10
c.512C>T	A171V					6-33435154-C-T	1	6.20e-7	-6.437	Likely Benign	0.434	Ambiguous	Likely Benign	0.052	Likely Benign										-1.65	Neutral	0.118	Benign	0.026	Benign	4.15	Benign	0.03	Affected	3.74	4	0	0	2.4	28.05
c.514C>T	R172W		Uncertain		2	6-33435156-C-T	9	5.58e-6	-10.258	Likely Pathogenic	0.877	Likely Pathogenic	Ambiguous	0.228	Likely Benign										-3.61	Deleterious	0.997	Probably Damaging	0.803	Possibly Damaging	3.95	Benign	0.00	Affected	3.61	5	2	-3	3.6	30.03
c.515G>A	R172Q		Uncertain		1	6-33435157-G-A	3	1.86e-6	-7.245	In-Between	0.465	Ambiguous	Likely Benign	0.135	Likely Benign										-1.72	Neutral	0.804	Possibly Damaging	0.091	Benign	4.04	Benign	0.04	Affected	3.61	5	1	1	1.0	-28.06
c.520A>G	M174V					6-33435162-A-G	2	1.24e-6	-8.604	Likely Pathogenic	0.897	Likely Pathogenic	Ambiguous	0.108	Likely Benign										-1.76	Neutral	0.213	Benign	0.067	Benign	4.12	Benign	0.04	Affected	3.61	5	1	2	2.3	-32.06
c.522G>A	M174I					6-33435164-G-A	4	2.48e-6	-8.732	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.120	Likely Benign										-1.63	Neutral	0.213	Benign	0.067	Benign	4.10	Benign	0.07	Tolerated	3.61	5	1	2	2.6	-18.03
c.524A>C	Q175P					6-33435166-A-C	1	6.20e-7	-6.995	Likely Benign	0.432	Ambiguous	Likely Benign	0.211	Likely Benign										1.55	Neutral	0.396	Benign	0.188	Benign	4.20	Benign	1.00	Tolerated	3.61	5	-1	0	1.9	-31.01
c.526A>C	S176R		Uncertain		1				-6.492	Likely Benign	0.987	Likely Pathogenic	Likely Pathogenic	0.247	Likely Benign										0.94	Neutral	0.718	Possibly Damaging	0.168	Benign	4.16	Benign	0.87	Tolerated			0	-1	-3.7	69.11
c.526A>G	S176G		Uncertain		1	6-33435168-A-G	1	6.20e-7	-7.541	In-Between	0.360	Ambiguous	Likely Benign	0.066	Likely Benign										-1.08	Neutral	0.131	Benign	0.039	Benign	4.08	Benign	0.22	Tolerated	3.54	6	0	1	0.4	-30.03
c.527G>A	S176N					6-33435169-G-A	1	6.20e-7	-6.286	Likely Benign	0.594	Likely Pathogenic	Likely Benign	0.070	Likely Benign										-0.56	Neutral	0.421	Benign	0.080	Benign	4.10	Benign	0.22	Tolerated	3.54	6	1	1	-2.7	27.03
c.52T>A	Y18N					6-33420316-T-A			-3.094	Likely Benign	0.492	Ambiguous	Likely Benign	0.075	Likely Benign										-0.73	Neutral	0.872	Possibly Damaging	0.114	Benign	4.07	Benign	0.00	Affected	4.32	1	-2	-2	-2.2	-49.07
c.52T>C	Y18H					6-33420316-T-C			-2.871	Likely Benign	0.541	Ambiguous	Likely Benign	0.045	Likely Benign										-0.58	Neutral	0.872	Possibly Damaging	0.114	Benign	4.07	Benign	0.00	Affected	4.32	1	2	0	-1.9	-26.03
c.533A>G	K178R					6-33435175-A-G	1	6.20e-7	-4.398	Likely Benign	0.281	Likely Benign	Likely Benign	0.117	Likely Benign										-1.62	Neutral	0.905	Possibly Damaging	0.393	Benign	3.98	Benign	0.14	Tolerated	3.54	6	2	3	-0.6	28.01
c.53A>C	Y18S					6-33420317-A-C			-1.061	Likely Benign	0.280	Likely Benign	Likely Benign	0.124	Likely Benign										-0.50	Neutral	0.389	Benign	0.036	Benign	4.09	Benign	0.00	Affected	4.32	1	-2	-3	0.5	-76.10
c.53A>G	Y18C		Uncertain		1	6-33420317-A-G	44	2.88e-5	-2.658	Likely Benign	0.251	Likely Benign	Likely Benign	0.102	Likely Benign										-0.56	Neutral	0.872	Possibly Damaging	0.206	Benign	4.04	Benign	0.00	Affected	4.32	1	0	-2	3.8	-60.04
c.541C>T	H181Y					6-33435183-C-T	2	1.24e-6	-9.477	Likely Pathogenic	0.551	Ambiguous	Likely Benign	0.161	Likely Benign										-2.36	Neutral	0.818	Possibly Damaging	0.255	Benign	4.13	Benign	0.02	Affected	3.54	6	2	0	1.9	26.03
c.558G>C	L186F		Uncertain		1				-11.861	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.132	Likely Benign										-3.03	Deleterious	0.009	Benign	0.012	Benign	3.50	Benign	0.00	Affected			2	0	-1.0	34.02
c.55G>C	A19P					6-33420319-G-C			-3.579	Likely Benign	0.184	Likely Benign	Likely Benign	0.033	Likely Benign										0.09	Neutral	0.001	Benign	0.000	Benign	4.07	Benign	0.00	Affected	4.32	1	-1	1	-3.4	26.04
c.560T>C	L187P					6-33435202-T-C	1	6.20e-7	-13.192	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.320	Likely Benign										-5.17	Deleterious	0.917	Possibly Damaging	0.548	Possibly Damaging	3.70	Benign	0.01	Affected	3.47	9	-3	-3	-5.4	-16.04
c.56C>A	A19D					6-33420320-C-A	2	1.30e-6	-3.746	Likely Benign	0.573	Likely Pathogenic	Likely Benign	0.055	Likely Benign										-0.08	Neutral	0.588	Possibly Damaging	0.054	Benign	4.07	Benign	0.00	Affected	4.32	1	-2	0	-5.3	44.01
c.56C>T	A19V					6-33420320-C-T			-3.157	Likely Benign	0.095	Likely Benign	Likely Benign	0.063	Likely Benign										0.42	Neutral	0.371	Benign	0.036	Benign	4.27	Benign	0.00	Affected	4.32	1	0	0	2.4	28.05
c.583G>C	A195P		Likely Pathogenic		1				-9.715	Likely Pathogenic	0.978	Likely Pathogenic	Likely Pathogenic	0.152	Likely Benign										-3.03	Deleterious	0.997	Probably Damaging	0.916	Probably Damaging	4.00	Benign	0.04	Affected	3.54	6	1	-1	-3.4	26.04
c.583G>T	A195S					6-33435225-G-T	1	6.20e-7	-4.936	Likely Benign	0.618	Likely Pathogenic	Likely Benign	0.078	Likely Benign										-1.13	Neutral	0.990	Probably Damaging	0.760	Possibly Damaging	4.10	Benign	0.08	Tolerated	3.54	6	1	1	-2.6	16.00
c.58C>A	P20T					6-33420322-C-A			-3.258	Likely Benign	0.223	Likely Benign	Likely Benign	0.065	Likely Benign										-0.50	Neutral	0.909	Possibly Damaging	0.641	Possibly Damaging	4.28	Benign	0.00	Affected	4.32	1	-1	0	0.9	3.99
c.58C>T	P20S					6-33420322-C-T			-3.054	Likely Benign	0.153	Likely Benign	Likely Benign	0.076	Likely Benign										-0.25	Neutral	0.909	Possibly Damaging	0.641	Possibly Damaging	4.30	Benign	0.00	Affected	4.32	1	-1	1	0.8	-10.04
c.59C>A	P20H					6-33420323-C-A			-4.450	Likely Benign	0.352	Ambiguous	Likely Benign	0.132	Likely Benign										-0.69	Neutral	0.992	Probably Damaging	0.893	Possibly Damaging	4.23	Benign	0.00	Affected	4.32	1	-2	0	-1.6	40.02
c.59C>G	P20R		Uncertain		1				-3.548	Likely Benign	0.434	Ambiguous	Likely Benign	0.146	Likely Benign										-0.15	Neutral	0.972	Probably Damaging	0.804	Possibly Damaging	4.33	Benign	0.00	Affected	4.32	1	0	-2	-2.9	59.07
c.59C>T	P20L		Uncertain		3				-3.289	Likely Benign	0.464	Ambiguous	Likely Benign	0.100	Likely Benign										-0.44	Neutral	0.909	Possibly Damaging	0.713	Possibly Damaging	4.27	Benign	0.00	Affected	4.32	1	-3	-3	5.4	16.04
c.5G>A	S2N		Uncertain		2	6-33420269-G-A	3	1.96e-6	-4.104	Likely Benign	0.207	Likely Benign	Likely Benign	0.092	Likely Benign										-0.36	Neutral	0.000	Benign	0.000	Benign	4.06	Benign	0.00	Affected	4.32	1	1	1	-2.7	27.03
c.5G>C	S2T					6-33420269-G-C			-4.443	Likely Benign	0.144	Likely Benign	Likely Benign	0.051	Likely Benign										-0.55	Neutral	0.052	Benign	0.004	Benign	4.09	Benign	0.00	Affected	4.32	1	1	1	0.1	14.03
c.5G>T	S2I					6-33420269-G-T			-4.947	Likely Benign	0.439	Ambiguous	Likely Benign	0.031	Likely Benign										-0.59	Neutral	0.212	Benign	0.020	Benign	4.04	Benign	0.00	Affected	4.32	1	-2	-1	5.3	26.08
c.61T>A	F21I					6-33420325-T-A			-3.678	Likely Benign	0.678	Likely Pathogenic	Likely Benign	0.141	Likely Benign										0.56	Neutral	0.462	Possibly Damaging	0.307	Benign	4.29	Benign	0.00	Affected	4.32	1	0	1	1.7	-34.02
c.61T>C	F21L					6-33420325-T-C			-2.480	Likely Benign	0.940	Likely Pathogenic	Ambiguous	0.140	Likely Benign										0.15	Neutral	0.140	Benign	0.153	Benign	4.34	Benign	0.00	Affected	4.32	1	0	2	1.0	-34.02
c.61T>G	F21V					6-33420325-T-G			-2.823	Likely Benign	0.563	Ambiguous	Likely Benign	0.224	Likely Benign										0.64	Neutral	0.462	Possibly Damaging	0.307	Benign	4.44	Benign	0.00	Affected	4.32	1	-1	-1	1.4	-48.04
c.62T>A	F21Y					6-33420326-T-A			-3.712	Likely Benign	0.351	Ambiguous	Likely Benign	0.088	Likely Benign										-0.23	Neutral	0.273	Benign	0.153	Benign	4.15	Benign	0.00	Affected	4.32	1	3	7	-4.1	16.00
c.63C>A	F21L					6-33420327-C-A			-2.480	Likely Benign	0.940	Likely Pathogenic	Ambiguous	0.103	Likely Benign										0.15	Neutral	0.140	Benign	0.153	Benign	4.34	Benign	0.00	Affected	4.32	1	0	2	1.0	-34.02
c.64A>G	R22G					6-33420328-A-G			-3.628	Likely Benign	0.322	Likely Benign	Likely Benign	0.185	Likely Benign										-0.42	Neutral	0.462	Possibly Damaging	0.152	Benign	4.19	Benign	0.00	Affected	4.32	1	-2	-3	4.1	-99.14
c.65G>A	R22K					6-33420329-G-A			-4.736	Likely Benign	0.268	Likely Benign	Likely Benign	0.032	Likely Benign										-0.12	Neutral	0.140	Benign	0.067	Benign	4.27	Benign	0.00	Affected	4.32	1	2	3	0.6	-28.01
c.66A>T	R22S					6-33420330-A-T			-3.419	Likely Benign	0.602	Likely Pathogenic	Likely Benign	0.190	Likely Benign										0.01	Neutral	0.462	Possibly Damaging	0.227	Benign	4.28	Benign	0.00	Affected	4.32	1	-1	0	3.7	-69.11
c.67G>T	D23Y					6-33420331-G-T			-4.191	Likely Benign	0.729	Likely Pathogenic	Likely Benign	0.142	Likely Benign										-2.87	Deleterious	0.972	Probably Damaging	0.861	Possibly Damaging	3.46	Benign	0.00	Affected	4.32	1	-3	-4	2.2	48.09
c.69T>G	D23E					6-33423478-T-G	15	9.29e-6	-3.329	Likely Benign	0.565	Likely Pathogenic	Likely Benign	0.084	Likely Benign										-1.35	Neutral	0.643	Possibly Damaging	0.417	Benign	3.59	Benign	0.00	Affected	4.32	1	2	3	0.0	14.03
c.6C>A	S2R					6-33420270-C-A	1	6.52e-7	-3.684	Likely Benign	0.426	Ambiguous	Likely Benign	0.070	Likely Benign										-0.44	Neutral	0.117	Benign	0.008	Benign	4.05	Benign	0.00	Affected	4.32	1	-1	0	-3.7	69.11
c.70G>A	V24I					6-33423479-G-A	9	5.58e-6	-3.701	Likely Benign	0.137	Likely Benign	Likely Benign	0.069	Likely Benign										-0.25	Neutral	0.043	Benign	0.031	Benign	3.96	Benign	0.00	Affected	4.32	1	3	4	0.3	14.03
c.73C>T	R25W		Uncertain		2	6-33423482-C-T	6	3.72e-6	-5.133	Likely Benign	0.549	Ambiguous	Likely Benign	0.158	Likely Benign										-1.60	Neutral	0.994	Probably Damaging	0.919	Probably Damaging	3.92	Benign	0.00	Affected	4.32	1	-3	2	3.6	30.03
c.74G>A	R25Q		Uncertain		1	6-33423483-G-A	15	9.29e-6	-4.126	Likely Benign	0.211	Likely Benign	Likely Benign	0.038	Likely Benign										-0.70	Neutral	0.829	Possibly Damaging	0.614	Possibly Damaging	4.01	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06
c.76G>A	G26R		Benign		1	6-33423485-G-A	3	1.86e-6	-2.946	Likely Benign	0.678	Likely Pathogenic	Likely Benign	0.189	Likely Benign										-2.22	Neutral	0.994	Probably Damaging	0.990	Probably Damaging	3.87	Benign	0.00	Affected	4.32	1	-3	-2	-4.1	99.14
c.77G>T	G26V					6-33423486-G-T	1	6.20e-7	-3.499	Likely Benign	0.165	Likely Benign	Likely Benign	0.197	Likely Benign										-2.34	Neutral	0.994	Probably Damaging	0.990	Probably Damaging	3.89	Benign	0.00	Affected	4.32	1	-3	-1	4.6	42.08
c.79C>T	P27S					6-33423488-C-T	1	6.20e-7	-2.891	Likely Benign	0.098	Likely Benign	Likely Benign	0.063	Likely Benign										-2.01	Neutral	0.909	Possibly Damaging	0.901	Possibly Damaging	3.91	Benign	0.00	Affected	4.32	1	-1	1	0.8	-10.04
c.7A>G	R3G					6-33420271-A-G			-3.093	Likely Benign	0.160	Likely Benign	Likely Benign	0.099	Likely Benign										-0.20	Neutral	0.115	Benign	0.018	Benign	3.99	Benign	0.00	Affected	4.32	1	-2	-3	4.1	-99.14
c.82T>C	S28P		Uncertain		1				-3.309	Likely Benign	0.051	Likely Benign	Likely Benign	0.047	Likely Benign										1.37	Neutral	0.000	Benign	0.000	Benign	4.53	Benign	0.00	Affected	4.32	1	1	-1	-0.8	10.04
c.85A>G	M29V					6-33423494-A-G	1	6.20e-7	-1.841	Likely Benign	0.057	Likely Benign	Likely Benign	0.209	Likely Benign										-0.39	Neutral	0.006	Benign	0.091	Benign	4.27	Benign	0.00	Affected	4.32	1	1	2	2.3	-32.06
c.86T>C	M29T		Uncertain		1				-2.167	Likely Benign	0.122	Likely Benign	Likely Benign	0.199	Likely Benign										-0.37	Neutral	0.018	Benign	0.184	Benign	4.33	Benign	0.00	Affected	4.32	1	-1	-1	-2.6	-30.09
c.87G>A	M29I					6-33423496-G-A	6	3.72e-6	-2.425	Likely Benign	0.185	Likely Benign	Likely Benign	0.067	Likely Benign										-0.51	Neutral	0.006	Benign	0.091	Benign	4.26	Benign	0.00	Affected	4.32	1	1	2	2.6	-18.03
c.88C>T	H30Y		Uncertain		1				-3.047	Likely Benign	0.115	Likely Benign	Likely Benign	0.082	Likely Benign										-1.84	Neutral	0.273	Benign	0.478	Possibly Damaging	3.99	Benign	0.00	Affected	4.32	1	0	2	1.9	26.03
c.90C>A	H30Q					6-33423499-C-A	1	6.20e-7	-3.016	Likely Benign	0.141	Likely Benign	Likely Benign	0.068	Likely Benign										-2.21	Neutral	0.462	Possibly Damaging	0.599	Possibly Damaging	3.93	Benign	0.00	Affected	4.32	1	0	3	-0.3	-9.01
c.92G>A	R31Q		Uncertain		1	6-33423501-G-A	7	4.34e-6	-4.434	Likely Benign	0.136	Likely Benign	Likely Benign	0.051	Likely Benign										-0.92	Neutral	0.829	Possibly Damaging	0.614	Possibly Damaging	4.01	Benign	0.00	Affected	4.32	1	1	1	1.0	-28.06
c.95C>A	T32N					6-33423504-C-A	2	1.24e-6	-3.466	Likely Benign	0.090	Likely Benign	Likely Benign	0.040	Likely Benign										-1.01	Neutral	0.604	Possibly Damaging	0.140	Benign	4.15	Benign	0.00	Affected	4.32	1	0	0	-2.8	13.00
c.95C>T	T32I					6-33423504-C-T	1	6.20e-7	-3.689	Likely Benign	0.213	Likely Benign	Likely Benign	0.024	Likely Benign										-0.57	Neutral	0.049	Benign	0.026	Benign	4.26	Benign	0.00	Affected	4.32	1	-1	0	5.2	12.05
c.9G>T	R3S					6-33420273-G-T	1	6.50e-7	-2.296	Likely Benign	0.310	Likely Benign	Likely Benign	0.111	Likely Benign										-0.53	Neutral	0.115	Benign	0.013	Benign	4.02	Benign	0.00	Affected	4.32	1	-1	0	3.7	-69.11
c.1712C>T	S571L (3D Viewer)	GAP				6-33440764-C-T	1	6.23e-7	-11.651	Likely Pathogenic	0.660	Likely Pathogenic	Likely Benign	0.841	Likely Pathogenic	-1.53	Ambiguous	0.1	-1.05	Ambiguous	-1.29	Ambiguous	0.27	Likely Benign	-5.61	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	-1.25	Pathogenic	0.04	Affected	3.37	35	-2	-3	4.6	26.08
c.1202G>T	R401L (3D Viewer)	C2				6-33438107-G-T	1	6.20e-7	-12.280	Likely Pathogenic	0.972	Likely Pathogenic	Likely Pathogenic	0.858	Likely Pathogenic	-1.52	Ambiguous	0.1	-0.23	Likely Benign	-0.88	Ambiguous	0.22	Likely Benign	-6.42	Deleterious	0.997	Probably Damaging	0.987	Probably Damaging	5.44	Benign	0.02	Affected	3.38	27	-2	-3	8.3	-43.03
c.1468G>C	A490P (3D Viewer)	GAP	Uncertain		1				-12.905	Likely Pathogenic	0.941	Likely Pathogenic	Ambiguous	0.878	Likely Pathogenic	-1.27	Ambiguous	0.1	1.31	Ambiguous	0.02	Likely Benign	1.07	Destabilizing	-4.81	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	-1.42	Pathogenic	0.01	Affected	3.37	35	-1	1	-3.4	26.04
c.1559C>T	S520F (3D Viewer)	GAP	Uncertain		1				-12.541	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.833	Likely Pathogenic	-1.20	Ambiguous	0.4	0.39	Likely Benign	-0.41	Likely Benign	0.25	Likely Benign	-5.57	Deleterious	0.999	Probably Damaging	0.996	Probably Damaging	-1.36	Pathogenic	0.00	Affected	3.37	35	-2	-3	3.6	60.10
c.1042G>A	V348M (3D Viewer)	C2	Uncertain		1				-7.076	In-Between	0.546	Ambiguous	Likely Benign	0.191	Likely Benign	-1.19	Ambiguous	0.1	0.72	Ambiguous	-0.24	Likely Benign	0.76	Ambiguous	-1.62	Neutral	0.966	Probably Damaging	0.564	Possibly Damaging	1.58	Pathogenic	0.03	Affected	3.37	25	2	1	-2.3	32.06	253.8	-47.4	-0.3	0.1	0.2	0.1						X		Potentially Benign	The iso-propyl side chain of Val348, located in an anti-parallel β sheet strand (res. Gly341-Pro349), packs against multiple hydrophobic C2 domain residues (e.g., Leu353, Leu323, Leu402). In the variant simulations, the thioether side chain of Met348 can form similar interactions as valine due to its comparable hydrophobic profile. In fact, the thioether group of methionine can even stack favorably with the phenol ring of Tyr363 in the anti-parallel β sheet strand (res. Ala399-Ile411). Overall, the residue swap does not appear to cause negative effects on the protein structure based on the simulations.
c.1673A>G	H558R (3D Viewer)	GAP	Uncertain		1				-14.445	Likely Pathogenic	0.554	Ambiguous	Likely Benign	0.587	Likely Pathogenic	-1.14	Ambiguous	0.1	-0.23	Likely Benign	-0.69	Ambiguous	1.03	Destabilizing	-4.94	Deleterious	0.677	Possibly Damaging	0.239	Benign	-1.24	Pathogenic	0.14	Tolerated	3.37	35	0	2	-1.3	19.05
c.1339G>C	V447L (3D Viewer)	GAP	Uncertain		1				-5.136	Likely Benign	0.491	Ambiguous	Likely Benign	0.180	Likely Benign	-1.13	Ambiguous	0.1	0.54	Ambiguous	-0.30	Likely Benign	0.03	Likely Benign	-0.29	Neutral	0.947	Possibly Damaging	0.851	Possibly Damaging	3.61	Benign	0.90	Tolerated	3.37	32	1	2	-0.4	14.03
c.1198G>A	V400M (3D Viewer)	C2				6-33438103-G-A	3	1.86e-6	-5.438	Likely Benign	0.573	Likely Pathogenic	Likely Benign	0.443	Likely Benign	-1.12	Ambiguous	0.1	-0.16	Likely Benign	-0.64	Ambiguous	0.55	Ambiguous	-1.44	Neutral	0.868	Possibly Damaging	0.289	Benign	5.26	Benign	0.01	Affected	3.38	27	1	2	-2.3	32.06
c.1660G>A	V554M (3D Viewer)	GAP				6-33438903-G-A	1	6.20e-7	-8.118	Likely Pathogenic	0.671	Likely Pathogenic	Likely Benign	0.217	Likely Benign	-1.11	Ambiguous	0.0	-0.20	Likely Benign	-0.66	Ambiguous	0.73	Ambiguous	-2.26	Neutral	0.994	Probably Damaging	0.867	Possibly Damaging	3.22	Benign	0.00	Affected	3.37	35	1	2	-2.3	32.06
c.2072C>T	T691I (3D Viewer)	GAP				6-33441331-C-T	1	6.20e-7	-5.857	Likely Benign	0.202	Likely Benign	Likely Benign	0.052	Likely Benign	-1.08	Ambiguous	0.1	-2.12	Stabilizing	-1.60	Ambiguous	-0.61	Ambiguous	-1.19	Neutral	0.040	Benign	0.003	Benign	3.49	Benign	0.34	Tolerated	3.43	14	-1	0	5.2	12.05
c.1811C>T	S604L (3D Viewer)	GAP	Uncertain		1	6-33440863-C-T	6	3.72e-6	-14.683	Likely Pathogenic	0.965	Likely Pathogenic	Likely Pathogenic	0.639	Likely Pathogenic	-0.94	Ambiguous	0.1	-1.24	Ambiguous	-1.09	Ambiguous	-0.31	Likely Benign	-5.97	Deleterious	1.000	Probably Damaging	0.991	Probably Damaging	3.09	Benign	0.00	Affected	3.37	35	-3	-2	4.6	26.08	234.0	-49.6	0.0	0.1	0.3	0.5	X			X				Potentially Pathogenic	Ser604 is located in a short turn between an α helix (res. Glu582-Met603) and a short α helical section (res. Ser606-Phe608). In the WT simulations, the hydroxyl side chain of Ser604 periodically hydrogen bonds with the backbone carbonyl groups of other α helix residues (e.g., Pro600, Met603). Serine weakens the α helix secondary structure, and thus, Ser604 along with Pro605 breaks the α helix, facilitating the turn in the WT structure.In contrast, in the variant simulations, Leu604 forms a few hydrophobic interactions (e.g., Leu607, Phe608). More importantly, the helix end is more stable than with Ser604 in the WT. The residue swap could have a more profound effect on the actual folding process, for example, by preventing the bending at the α helix end, than what the simulations suggest.Moreover, Ser604 directly hydrogen bonds with Ras residues Ser65 and Ala66 in the WT SynGAP-Ras complex. The hydrophobic leucine cannot maintain these interactions with Ras at the GAP-Ras interface. Thus, the effect of the residue swap on the complex formation with the GTPase cannot be fully explored in the solvent-only simulations.
c.1976C>T	S659F (3D Viewer)	GAP	Uncertain		1				-10.925	Likely Pathogenic	0.662	Likely Pathogenic	Likely Benign	0.194	Likely Benign	-0.81	Ambiguous	0.1	-0.25	Likely Benign	-0.53	Ambiguous	0.32	Likely Benign	-4.59	Deleterious	0.806	Possibly Damaging	0.171	Benign	3.39	Benign	0.05	Affected	3.38	28	-3	-2	3.6	60.10	221.3	-61.2	0.0	0.0	0.6	0.4						X		Potentially Benign	In the WT simulations, the hydroxyl group of Ser659, located in a kink in the middle of the long α-helix (res. Ser641-Glu666), forms a hydrogen bond with the carboxylate group of Glu656. However, the phenol ring of the Phe659 side chain cannot form a similar hydrogen bond. Instead, it interacts with the hydrophobic isopropyl side chain of Val555 from the opposing α-helix (res. Ala533-Val560). This residue swap may therefore cause issues during protein folding.
c.1918A>T	T640S (3D Viewer)	GAP	Uncertain		1	6-33441177-A-T	1	6.20e-7	-2.371	Likely Benign	0.062	Likely Benign	Likely Benign	0.088	Likely Benign	-0.78	Ambiguous	0.1	0.43	Likely Benign	-0.18	Likely Benign	-0.30	Likely Benign	0.92	Neutral	0.000	Benign	0.001	Benign	3.60	Benign	0.33	Tolerated	3.37	30	1	1	-0.1	-14.03
c.1579G>T	D527Y (3D Viewer)	GAP	Uncertain		1				-15.386	Likely Pathogenic	0.978	Likely Pathogenic	Likely Pathogenic	0.905	Likely Pathogenic	-0.77	Ambiguous	0.2	1.89	Ambiguous	0.56	Ambiguous	-0.14	Likely Benign	-8.79	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-2.41	Pathogenic	0.00	Affected	3.37	35	-4	-3	2.2	48.09	270.9	-45.7	0.1	0.1	-0.1	0.0		X						Potentially Pathogenic	Asp527 is located on an α-α loop between the two α-helices (res. Gly502-Tyr518 and Ala533-Val560). In the WT simulations, the carboxylate group of the Asp527 side chain forms hydrogen bonds with the backbone atoms of loop residues (e.g., Ile529, Lys530) facing the membrane surface. In the variant simulations, Tyr527 is a bulkier residue that faces away from the loop and stacks with Phe646 in a nearby α-helix (res. Ser614-Ser668). Regardless, no negative structural effects are observed during the variant simulations. However, due to its location near the SynGAP-membrane interface, the effect of the residue swap cannot be fully addressed using the SynGAP solvent-only simulations.
c.707C>A	A236E (3D Viewer)	PH				6-33435558-C-A	1	6.20e-7	-10.844	Likely Pathogenic	0.835	Likely Pathogenic	Ambiguous	0.844	Likely Pathogenic	-0.75	Ambiguous	0.2	0.28	Likely Benign	-0.24	Likely Benign	1.08	Destabilizing	-4.24	Deleterious	0.998	Probably Damaging	0.900	Possibly Damaging	6.06	Benign	0.02	Affected	3.40	14	-1	0	-5.3	58.04
c.1093G>T	V365L (3D Viewer)	C2				6-33437998-G-T	5	3.31e-6	-6.141	Likely Benign	0.265	Likely Benign	Likely Benign	0.065	Likely Benign	-0.72	Ambiguous	0.2	0.74	Ambiguous	0.01	Likely Benign	0.35	Likely Benign	-1.71	Neutral	0.005	Benign	0.003	Benign	2.50	Benign	0.25	Tolerated	3.38	21	1	2	-0.4	14.03
c.1198G>C	V400L (3D Viewer)	C2	Benign		1	6-33438103-G-C	22	1.36e-5	-1.000	Likely Benign	0.137	Likely Benign	Likely Benign	0.325	Likely Benign	-0.71	Ambiguous	0.2	0.39	Likely Benign	-0.16	Likely Benign	-0.29	Likely Benign	-0.60	Neutral	0.001	Benign	0.001	Benign	5.33	Benign	0.64	Tolerated	3.38	27	2	1	-0.4	14.03	251.0	-30.1	0.0	0.0	0.7	0.1						X		Potentially Benign	The iso-propyl side chain of Val400, located in an anti-parallel β sheet strand (res. Ala399-Ile411), hydrophobically packs against hydrophobic residues within the anti-parallel β sheet of the C2 domain (e.g., Ile268, Ala404, Leu325, Leu402). Val400 is swapped for another hydrophobic residue, leucine, whose branched hydrocarbon side chain is of a comparable size and thus packs favorably within the C2 domain. In short, the residue swap has no apparent negative effect on the structure based on the variant simulations.	10.1016/j.ajhg.2020.11.011
c.1076C>T	T359I (3D Viewer)	C2				6-33437981-C-T	1	6.22e-7	-2.594	Likely Benign	0.181	Likely Benign	Likely Benign	0.085	Likely Benign	-0.66	Ambiguous	0.1	-0.64	Ambiguous	-0.65	Ambiguous	-0.63	Ambiguous	0.77	Neutral	0.070	Benign	0.006	Benign	1.80	Pathogenic	0.23	Tolerated	3.38	24	-1	0	5.2	12.05
c.662A>T	E221V (3D Viewer)	PH	Likely Pathogenic		1				-14.954	Likely Pathogenic	0.987	Likely Pathogenic	Likely Pathogenic	0.875	Likely Pathogenic	-0.66	Ambiguous	0.2	-0.89	Ambiguous	-0.78	Ambiguous	0.49	Likely Benign	-5.54	Deleterious	0.596	Possibly Damaging	0.203	Benign	5.86	Benign	0.00	Affected	3.41	13	-2	-2	7.7	-29.98	234.5	50.6	0.0	0.0	-0.4	0.2		X						Uncertain	The introduced residue Val221 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Unlike the carboxylate group of Glu221, Val221 cannot form hydrogen bonds with Thr223 or a salt bridge with the amino group of the Lys207 side chain. Despite this, the WT simulations containing Glu221 do not show significant differences compared to the variant simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1093G>A	V365I (3D Viewer)	C2				6-33437998-G-A	4	2.65e-6	-5.943	Likely Benign	0.155	Likely Benign	Likely Benign	0.036	Likely Benign	-0.65	Ambiguous	0.2	-0.11	Likely Benign	-0.38	Likely Benign	0.13	Likely Benign	-0.47	Neutral	0.451	Benign	0.137	Benign	1.76	Pathogenic	0.10	Tolerated	3.38	21	3	4	0.3	14.03
c.1097C>T	T366I (3D Viewer)	C2				6-33438002-C-T	1	6.20e-7	-4.921	Likely Benign	0.279	Likely Benign	Likely Benign	0.058	Likely Benign	-0.62	Ambiguous	0.1	-0.31	Likely Benign	-0.47	Likely Benign	-0.14	Likely Benign	-1.22	Neutral	0.002	Benign	0.001	Benign	1.77	Pathogenic	0.26	Tolerated	3.38	23	-1	0	5.2	12.05
c.2095G>A	V699M (3D Viewer)	GAP	Uncertain		2	6-33441354-G-A	8	4.96e-6	-8.869	Likely Pathogenic	0.484	Ambiguous	Likely Benign	0.276	Likely Benign	-0.58	Ambiguous	0.1	0.29	Likely Benign	-0.15	Likely Benign	0.96	Ambiguous	-2.18	Neutral	0.994	Probably Damaging	0.806	Possibly Damaging	3.37	Benign	0.03	Affected	3.47	10	2	1	-2.3	32.06	257.8	-47.2	0.0	0.0	0.9	0.1						X		Potentially Benign	The isopropyl side chain of Val699, located on an α-helix (res. Leu685-Gln702), packs against hydrophobic residues (e.g., Leu703, Leu696, Leu435, Leu439) in the inter-helix space. In the variant simulations, the thioether side chain of Met699 has similar physicochemical properties to Val699 in the WT, and thus, it is able to maintain similar interactions. Consequently, the mutation causes no apparent changes in the structure.
c.817G>A	E273K (3D Viewer)	C2				6-33437722-G-A	1	6.20e-7	-12.690	Likely Pathogenic	0.917	Likely Pathogenic	Ambiguous	0.205	Likely Benign	-0.57	Ambiguous	0.3	-0.38	Likely Benign	-0.48	Likely Benign	0.23	Likely Benign	-2.66	Deleterious	0.896	Possibly Damaging	0.415	Benign	1.77	Pathogenic	0.12	Tolerated	3.38	18	1	0	-0.4	-0.94
c.1555G>A	E519K (3D Viewer)	GAP				6-33438798-G-A	1	6.20e-7	-13.532	Likely Pathogenic	0.970	Likely Pathogenic	Likely Pathogenic	0.328	Likely Benign	-0.55	Ambiguous	0.0	-0.60	Ambiguous	-0.58	Ambiguous	0.06	Likely Benign	-3.48	Deleterious	0.996	Probably Damaging	0.987	Probably Damaging	3.28	Benign	0.03	Affected	3.37	35	1	0	-0.4	-0.94
c.1890C>G	I630M (3D Viewer)	GAP				6-33440942-C-G	1	6.20e-7	-10.586	Likely Pathogenic	0.259	Likely Benign	Likely Benign	0.508	Likely Pathogenic	-0.55	Ambiguous	0.1	0.32	Likely Benign	-0.12	Likely Benign	1.06	Destabilizing	-1.90	Neutral	0.833	Possibly Damaging	0.700	Possibly Damaging	-1.38	Pathogenic	0.02	Affected	3.37	34	1	2	-2.6	18.03
c.1441C>T	H481Y (3D Viewer)	GAP	Likely Benign		1	6-33438473-C-T	16	9.91e-6	-10.910	Likely Pathogenic	0.565	Likely Pathogenic	Likely Benign	0.256	Likely Benign	-0.53	Ambiguous	0.1	-0.46	Likely Benign	-0.50	Ambiguous	0.20	Likely Benign	-3.32	Deleterious	0.988	Probably Damaging	0.979	Probably Damaging	3.40	Benign	0.59	Tolerated	3.37	33	0	2	1.9	26.03	256.5	-44.4	0.0	0.0	0.2	0.2	X			X				Uncertain	The imidazole ring of the His481 side chain is located in a short helical structure (res. Glu480-Leu482) within an α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. In the WT simulations, His481 alternately stacks against Arg485, Arg587, and Glu480 without a definite role. In the variant simulations, Tyr481 also alternately stacks with nearby arginine residues, including Arg485, Arg587, and Arg479. The interaction between Tyr481 and Arg479 affects the α-α loop, causing it to fold into a distorted helical structure, an effect that might be more pronounced during protein folding. Finally, the potential effect of the residue swap on SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.2029A>T	S677C (3D Viewer)	GAP	Benign		1				-8.496	Likely Pathogenic	0.076	Likely Benign	Likely Benign	0.153	Likely Benign	-0.51	Ambiguous	0.3	-0.30	Likely Benign	-0.41	Likely Benign	0.15	Likely Benign	-2.41	Neutral	0.932	Possibly Damaging	0.222	Benign	3.25	Benign	0.04	Affected	3.41	23	-1	0	3.3	16.06
c.1678G>T	V560L (3D Viewer)	GAP				6-33440730-G-T	1	6.34e-7	-10.191	Likely Pathogenic	0.533	Ambiguous	Likely Benign	0.489	Likely Benign	-0.44	Likely Benign	0.0	0.48	Likely Benign	0.02	Likely Benign	0.45	Likely Benign	-2.45	Neutral	0.508	Possibly Damaging	0.209	Benign	-1.24	Pathogenic	0.40	Tolerated	3.37	35	1	2	-0.4	14.03
c.1600T>C	S534P (3D Viewer)	GAP				6-33438843-T-C	3	1.86e-6	-5.056	Likely Benign	0.265	Likely Benign	Likely Benign	0.203	Likely Benign	-0.40	Likely Benign	0.2	0.35	Likely Benign	-0.03	Likely Benign	0.47	Likely Benign	-3.81	Deleterious	0.993	Probably Damaging	0.993	Probably Damaging	3.32	Benign	0.05	Affected	3.37	35	-1	1	-0.8	10.04
c.1973G>A	G658D (3D Viewer)	GAP	Uncertain		1	6-33441232-G-A	3	1.86e-6	-7.786	In-Between	0.442	Ambiguous	Likely Benign	0.144	Likely Benign	-0.40	Likely Benign	0.1	-0.59	Ambiguous	-0.50	Ambiguous	0.46	Likely Benign	-2.64	Deleterious	0.008	Benign	0.005	Benign	3.53	Benign	0.38	Tolerated	3.39	24	1	-1	-3.1	58.04	219.8	-84.3	0.0	0.0	0.2	0.1						X		Potentially Pathogenic	Gly658, located on the outer surface of an α helix (res. Ser641-Glu666), weakens the helix integrity at that spot, which is necessary for the kink in the middle of the long helix. In the variant simulations, the carboxylic acid side chain of Asp658 is on the surface of the α helix and is not involved in any interactions. However, aspartate is not as effective a breaker of the secondary structure element as glycine, which may lead to misfolding.
c.1524T>A	D508E (3D Viewer)	GAP				6-33438556-T-A	1	6.20e-7	-5.959	Likely Benign	0.242	Likely Benign	Likely Benign	0.118	Likely Benign	-0.39	Likely Benign	0.1	0.99	Ambiguous	0.30	Likely Benign	0.59	Ambiguous	-3.16	Deleterious	0.005	Benign	0.006	Benign	3.43	Benign	0.20	Tolerated	3.37	35	2	3	0.0	14.03
c.1888A>C	I630L (3D Viewer)	GAP				6-33440940-A-C			-8.949	Likely Pathogenic	0.277	Likely Benign	Likely Benign	0.165	Likely Benign	-0.39	Likely Benign	0.0	0.23	Likely Benign	-0.08	Likely Benign	0.33	Likely Benign	-1.30	Neutral	0.102	Benign	0.108	Benign	-0.81	Pathogenic	0.27	Tolerated	3.37	34	2	2	-0.7	0.00
c.2168C>T	T723I (3D Viewer)	GAP	Likely Benign		1	6-33441633-C-T	2	1.24e-6	-2.591	Likely Benign	0.120	Likely Benign	Likely Benign	0.045	Likely Benign	-0.39	Likely Benign	0.0	-0.20	Likely Benign	-0.30	Likely Benign	0.26	Likely Benign	-2.09	Neutral	0.088	Benign	0.030	Benign	3.39	Benign	0.03	Affected	3.50	8	0	-1	5.2	12.05	252.3	-31.6	0.0	0.0	-0.2	0.2						X		Uncertain	The hydroxyl group of Thr723, located on the outer surface of an α-helix (res. Leu714-Arg726), continuously forms hydrogen bonds with the backbone carbonyl of Asn719 in the WT simulations, potentially lowering the stability of the α-helix. In the variant simulations, the sec-butyl side chain of Ile723 cannot form any hydrogen bonds, which, in theory, could increase the helix stability. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.862G>A	D288N (3D Viewer)	C2	Uncertain		1	6-33437767-G-A	2	1.24e-6	-10.535	Likely Pathogenic	0.521	Ambiguous	Likely Benign	0.321	Likely Benign	-0.39	Likely Benign	0.1	0.01	Likely Benign	-0.19	Likely Benign	-0.03	Likely Benign	-3.73	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	1.78	Pathogenic	0.05	Affected	3.38	23	1	2	0.0	-0.98
c.1421A>G	D474G (3D Viewer)	GAP				6-33438453-A-G	1	6.20e-7	-11.215	Likely Pathogenic	0.959	Likely Pathogenic	Likely Pathogenic	0.823	Likely Pathogenic	-0.38	Likely Benign	0.0	0.82	Ambiguous	0.22	Likely Benign	0.44	Likely Benign	-6.13	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.28	Pathogenic	0.07	Tolerated	3.37	34	-1	1	3.1	-58.04
c.1603A>C	S535R (3D Viewer)	GAP				6-33438846-A-C	3	1.86e-6	-9.363	Likely Pathogenic	0.913	Likely Pathogenic	Ambiguous	0.390	Likely Benign	-0.37	Likely Benign	0.0	-0.97	Ambiguous	-0.67	Ambiguous	0.64	Ambiguous	-1.99	Neutral	0.830	Possibly Damaging	0.274	Benign	-1.23	Pathogenic	0.19	Tolerated	3.37	35	-1	0	-3.7	69.11
c.1313C>T	A438V (3D Viewer)	GAP				6-33438218-C-T	3	1.86e-6	1.405	Likely Benign	0.073	Likely Benign	Likely Benign	0.046	Likely Benign	-0.36	Likely Benign	0.0	-0.70	Ambiguous	-0.53	Ambiguous	-1.21	Stabilizing	1.03	Neutral	0.000	Benign	0.000	Benign	4.45	Benign	0.97	Tolerated	3.38	26	0	0	2.4	28.05																10.1016/j.ajhg.2020.11.011
c.1069C>T	H357Y (3D Viewer)	C2				6-33437974-C-T	1	6.21e-7	-5.888	Likely Benign	0.168	Likely Benign	Likely Benign	0.140	Likely Benign	-0.33	Likely Benign	0.2	0.08	Likely Benign	-0.13	Likely Benign	-0.07	Likely Benign	-1.71	Neutral	0.936	Possibly Damaging	0.388	Benign	4.19	Benign	0.14	Tolerated	3.39	22	2	0	1.9	26.03
c.1315C>A	L439M (3D Viewer)	GAP				6-33438220-C-A	1	6.20e-7	-5.840	Likely Benign	0.363	Ambiguous	Likely Benign	0.187	Likely Benign	-0.33	Likely Benign	0.1	1.34	Ambiguous	0.51	Ambiguous	1.01	Destabilizing	-1.43	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	3.24	Benign	0.02	Affected	3.38	25	2	4	-1.9	18.03
c.1678G>A	V560M (3D Viewer)	GAP	Uncertain		2	6-33440730-G-A	15	9.50e-6	-9.598	Likely Pathogenic	0.516	Ambiguous	Likely Benign	0.520	Likely Pathogenic	-0.33	Likely Benign	0.1	0.88	Ambiguous	0.28	Likely Benign	0.72	Ambiguous	-2.42	Neutral	0.999	Probably Damaging	0.863	Possibly Damaging	-1.25	Pathogenic	0.14	Tolerated	3.37	35	2	1	-2.3	32.06	234.9	-52.6	0.0	0.0	-0.1	0.1						X		Potentially Benign	Val560 is located on the surface at the end of an α-helix (res. Ala533-Val560). The iso-propyl group of Val560 favorably packs against Asp508 of the opposing α-helix (res. Gln503-Glu519). However, in the variant simulations, the bulkier thioether side chain of Met560 does not form equally favorable inter-helix interactions. Regardless, no negative structural effects are observed during the simulations.
c.1950T>G	N650K (3D Viewer)	GAP				6-33441209-T-G			-13.078	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.269	Likely Benign	-0.33	Likely Benign	0.1	0.66	Ambiguous	0.17	Likely Benign	0.92	Ambiguous	-5.98	Deleterious	0.995	Probably Damaging	0.807	Possibly Damaging	3.02	Benign	0.03	Affected	3.37	30	0	1	-0.4	14.07
c.2105A>G	Q702R (3D Viewer)	GAP	Uncertain		1				-7.894	In-Between	0.348	Ambiguous	Likely Benign	0.294	Likely Benign	-0.31	Likely Benign	0.1	0.63	Ambiguous	0.16	Likely Benign	0.13	Likely Benign	-3.14	Deleterious	0.909	Possibly Damaging	0.889	Possibly Damaging	3.43	Benign	0.02	Affected	3.47	10	1	1	-1.0	28.06	270.3	-52.9	0.0	0.0	0.0	0.1		X						Potentially Pathogenic	The carboxamide side chain of Gln702 is located at the end and outer surface of an α-helix (res. Leu685-Gln702), where it does not directly form hydrogen bonds with any residues in the WT simulations. In the variant simulations, the positively charged guanidinium group of Arg702 forms a salt bridge with the negatively charged carboxylate group of Glu698 on the same helix and/or hydrogen bonds with the backbone carbonyl group of Ala438 on an opposite α-helix (res. Tyr428-Glu436). Consequently, the residue swap could strengthen the tertiary structure assembly, which could have either positive or negative effects on its function.
c.1594A>C	T532P (3D Viewer)	GAP	Benign		1				-2.143	Likely Benign	0.061	Likely Benign	Likely Benign	0.201	Likely Benign	-0.30	Likely Benign	0.2	0.06	Likely Benign	-0.12	Likely Benign	0.08	Likely Benign	-0.90	Neutral	0.005	Benign	0.008	Benign	-1.28	Pathogenic	0.18	Tolerated	3.37	35	0	-1	-0.9	-3.99	174.2	35.1	0.4	0.0	0.1	0.0						X		Potentially Benign	Thr532 is located on an α-α loop between the two α-helices (res. Gly502-Tyr518 and Ala533-Val560) facing the membrane. In the WT simulations, the hydroxyl group of Thr532 occasionally forms hydrogen bonds with the backbone atoms of other loop residues without any specific interaction. In the variant simulations, the Pro532 residue swap does not cause structural changes. Although hydrophilic residues seem more favorable in the loop, the pyrrolidine side chain of proline is well suited for unstructured protein regions such as loops. However, due to its location at the SynGAP-membrane interface, the effect of the residue swap cannot be fully addressed using the SynGAP solvent-only simulations.
c.1702G>T	V568L (3D Viewer)	GAP	Uncertain		1				-9.503	Likely Pathogenic	0.921	Likely Pathogenic	Ambiguous	0.651	Likely Pathogenic	-0.30	Likely Benign	0.3	0.57	Ambiguous	0.14	Likely Benign	0.56	Ambiguous	-2.69	Deleterious	0.511	Possibly Damaging	0.147	Benign	-1.23	Pathogenic	0.04	Affected	3.37	35	1	2	-0.4	14.03
c.899C>T	S300F (3D Viewer)	C2	Uncertain		1				-10.222	Likely Pathogenic	0.353	Ambiguous	Likely Benign	0.117	Likely Benign	-0.29	Likely Benign	0.4	0.16	Likely Benign	-0.07	Likely Benign	0.04	Likely Benign	-2.66	Deleterious	0.975	Probably Damaging	0.596	Possibly Damaging	1.52	Pathogenic	0.01	Affected	3.47	19	-3	-2	3.6	60.10	233.6	-67.6	-0.1	0.0	0.4	0.2	X	X						Potentially Pathogenic	The hydroxyl group of the Ser300 side chain, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Met289-Pro298, res. Thr305-Asn315), hydrogen bonds with the guanidinium group of Arg299 and the backbone amide group and side chain of Ser302. Thus, in the WT simulations, it contributes to the β hairpin stability. In the variant simulations, the phenol ring of Phe300 cannot form any side chain-related hydrogen bonds, and Arg299 is moved away from its central hairpin loop position.β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Due to its location near the membrane surface, the residue swap could also affect the C2 loop dynamics and SynGAP-membrane association. However, this is beyond the scope of the solvent-only simulations to unravel.
c.971G>T	R324L (3D Viewer)	C2				6-33437876-G-T	1	6.20e-7	-10.328	Likely Pathogenic	0.575	Likely Pathogenic	Likely Benign	0.489	Likely Benign	-0.28	Likely Benign	0.0	-0.08	Likely Benign	-0.18	Likely Benign	0.29	Likely Benign	-2.20	Neutral	0.999	Probably Damaging	0.997	Probably Damaging	1.86	Pathogenic	0.63	Tolerated	3.39	22	-2	-3	8.3	-43.03
c.1027G>A	V343I (3D Viewer)	C2	Uncertain		2	6-33437932-G-A	1	6.20e-7	-6.020	Likely Benign	0.117	Likely Benign	Likely Benign	0.020	Likely Benign	-0.27	Likely Benign	0.0	-0.04	Likely Benign	-0.16	Likely Benign	-0.39	Likely Benign	-0.14	Neutral	0.159	Benign	0.084	Benign	1.98	Pathogenic	0.27	Tolerated	3.37	25	4	3	0.3	14.03	240.2	-26.9	-0.2	0.2	-0.2	0.2						X		Potentially Benign	The iso-propyl side chain of Val343, located in an anti-parallel β sheet strand (res. Gly341-Pro349), is packing against multiple hydrophobic residues of the C2 domain (e.g., Leu327, Leu274, Val365). In the variant simulations, the sec-butyl side chain of Ile343 is basically able to form the same interactions as valine due to its similar hydrophobic profile. The residue swap also does not seem to cause negative effects on the protein structure based on the simulations.
c.1106C>G	T369R (3D Viewer)	C2				6-33438011-C-G	3	1.93e-6	-6.772	Likely Benign	0.571	Likely Pathogenic	Likely Benign	0.148	Likely Benign	-0.27	Likely Benign	0.1	1.48	Ambiguous	0.61	Ambiguous	0.29	Likely Benign	-2.15	Neutral	0.244	Benign	0.107	Benign	1.72	Pathogenic	0.32	Tolerated	3.42	19	-1	-1	-3.8	55.08
c.958G>A	V320I (3D Viewer)	C2	Uncertain		1				-5.220	Likely Benign	0.111	Likely Benign	Likely Benign	0.027	Likely Benign	-0.27	Likely Benign	0.2	0.66	Ambiguous	0.20	Likely Benign	0.01	Likely Benign	-0.21	Neutral	0.198	Benign	0.114	Benign	1.77	Pathogenic	0.45	Tolerated	3.38	23	3	4	0.3	14.03
c.958G>C	V320L (3D Viewer)	C2	Uncertain		1	6-33437863-G-C	6	3.72e-6	-6.207	Likely Benign	0.362	Ambiguous	Likely Benign	0.096	Likely Benign	-0.26	Likely Benign	0.2	1.33	Ambiguous	0.54	Ambiguous	0.51	Ambiguous	-1.02	Neutral	0.900	Possibly Damaging	0.373	Benign	1.78	Pathogenic	0.92	Tolerated	3.38	23	2	1	-0.4	14.03	245.8	-10.2	0.3	0.9	0.1	0.3						X		Potentially Benign	The isopropyl side chain of Val310, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Thr305-Asn315, res. Ala322-Asp330), hydrophobically packs with the side chains of nearby residues (e.g., Leu286, Val350, Pro318). The hydrophobic Leu320 side chain mostly forms the same interactions; hence, the residue swap does not seem to negatively affect the protein structure based on the variant simulations.
c.1135T>G	S379A (3D Viewer)	C2				6-33438040-T-G			-4.300	Likely Benign	0.077	Likely Benign	Likely Benign	0.217	Likely Benign	-0.22	Likely Benign	0.3	1.03	Ambiguous	0.41	Likely Benign	0.10	Likely Benign	-0.50	Neutral	0.012	Benign	0.002	Benign	3.91	Benign	0.21	Tolerated	4.32	11	1	1	2.6	-16.00
c.1585A>T	I529F (3D Viewer)	GAP				6-33438828-A-T	4	2.48e-6	-5.669	Likely Benign	0.235	Likely Benign	Likely Benign	0.320	Likely Benign	-0.21	Likely Benign	0.0	0.06	Likely Benign	-0.08	Likely Benign	0.06	Likely Benign	-0.97	Neutral	0.266	Benign	0.054	Benign	-1.30	Pathogenic	0.23	Tolerated	3.37	35	0	1	-1.7	34.02
c.597C>A	N199K (3D Viewer)	PH	Uncertain		1				-8.198	Likely Pathogenic	0.686	Likely Pathogenic	Likely Benign	0.024	Likely Benign	-0.19	Likely Benign	0.1	0.03	Likely Benign	-0.08	Likely Benign	0.33	Likely Benign	-1.48	Neutral	0.276	Benign	0.083	Benign	4.27	Benign	0.13	Tolerated	3.47	9	1	0	-0.4	14.07	207.8	21.5	-0.1	1.5	0.1	0.0						X		Uncertain	Asn199, located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by a positively charged lysine. On the protein surface, both the carboxamide group of Asn199 and the amino group of Lys199 side chains can form hydrogen bonds with the backbone carbonyl groups of residues (e.g., Ala249) at the end of an α helix (res. Ala236-Lys251). However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.607G>A	D203N (3D Viewer)	PH				6-33435249-G-A	1	6.20e-7	-7.465	In-Between	0.159	Likely Benign	Likely Benign	0.121	Likely Benign	-0.19	Likely Benign	0.1	-0.12	Likely Benign	-0.16	Likely Benign	-0.03	Likely Benign	-2.26	Neutral	0.970	Probably Damaging	0.749	Possibly Damaging	4.06	Benign	0.06	Tolerated	3.44	10	1	2	0.0	-0.98
c.1688G>T	R563M (3D Viewer)	GAP				6-33440740-G-T			-8.910	Likely Pathogenic	0.934	Likely Pathogenic	Ambiguous	0.311	Likely Benign	-0.18	Likely Benign	0.1	0.70	Ambiguous	0.26	Likely Benign	0.17	Likely Benign	-4.91	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	3.43	Benign	0.04	Affected	3.37	35	-1	0	6.4	-24.99
c.1223C>T	T408I (3D Viewer)	C2				6-33438128-C-T	1	6.19e-7	-10.023	Likely Pathogenic	0.542	Ambiguous	Likely Benign	0.131	Likely Benign	-0.16	Likely Benign	0.1	-0.67	Ambiguous	-0.42	Likely Benign	0.38	Likely Benign	-4.53	Deleterious	0.976	Probably Damaging	0.607	Possibly Damaging	4.08	Benign	0.05	Affected	3.38	28	-1	0	5.2	12.05
c.1322T>C	V441A (3D Viewer)	GAP	Conflicting		2	6-33438227-T-C	3	1.86e-6	-9.439	Likely Pathogenic	0.359	Ambiguous	Likely Benign	0.053	Likely Benign	-0.14	Likely Benign	0.0	0.33	Likely Benign	0.10	Likely Benign	0.95	Ambiguous	-2.92	Deleterious	0.513	Possibly Damaging	0.214	Benign	3.44	Benign	0.93	Tolerated	3.37	29	0	0	-2.4	-28.05	195.0	44.6	0.0	0.1	0.5	0.0				X		X		Uncertain	The iso-propyl side chain of Val441, located on the outer surface of an α helix (res. Asn440-Thr458), does not interact with other residues in the WT simulations. In the variant simulations, the methyl side chain of Ala441 is similarly hydrophobic and does not form any interactions on the outer helix surface. Although the residue swap does not negatively affect the protein structure based on the simulations, it is noteworthy that the residue faces the RasGTPase interface. Thus, the effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1966G>C	E656Q (3D Viewer)	GAP	Uncertain		1	6-33441225-G-C	1	6.20e-7	-9.145	Likely Pathogenic	0.766	Likely Pathogenic	Likely Benign	0.249	Likely Benign	-0.14	Likely Benign	0.0	-0.81	Ambiguous	-0.48	Likely Benign	0.25	Likely Benign	-2.29	Neutral	0.980	Probably Damaging	0.528	Possibly Damaging	3.46	Benign	0.02	Affected	3.39	24	2	2	0.0	-0.98	224.3	1.7	0.0	0.1	0.1	0.0		X						Potentially Benign	The carboxylate side chain of Glu656, located on an α helix (res. Ser641-Glu666), frequently forms a hydrogen bond with the nearby residue Ser659 on the same α helix. In the variant simulations, the carboxamide side chain of Gln656 alternatively forms a hydrogen bond with either Ser659 or Glu548 on an opposing helix (res. Ala533-Val560).Although the frequent interaction between Gln656 and Glu548 may strengthen or stabilize the tertiary structure assembly, the effect is likely to be marginal.
c.1573G>A	E525K (3D Viewer)	GAP				6-33438816-G-A	1	6.20e-7	-15.628	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.629	Likely Pathogenic	-0.13	Likely Benign	0.5	0.34	Likely Benign	0.11	Likely Benign	0.96	Ambiguous	-3.98	Deleterious	0.999	Probably Damaging	0.988	Probably Damaging	2.71	Benign	0.00	Affected	3.37	35	1	0	-0.4	-0.94
c.1585A>C	I529L (3D Viewer)	GAP				6-33438828-A-C	1	6.20e-7	0.920	Likely Benign	0.066	Likely Benign	Likely Benign	0.309	Likely Benign	-0.13	Likely Benign	0.0	-0.11	Likely Benign	-0.12	Likely Benign	-0.21	Likely Benign	0.00	Neutral	0.001	Benign	0.022	Benign	-1.24	Pathogenic	0.48	Tolerated	3.37	35	2	2	-0.7	0.00
c.1417G>A	V473I (3D Viewer)	GAP				6-33438449-G-A	1	6.20e-7	-7.481	In-Between	0.418	Ambiguous	Likely Benign	0.203	Likely Benign	-0.12	Likely Benign	0.0	1.20	Ambiguous	0.54	Ambiguous	-0.06	Likely Benign	-0.91	Neutral	0.929	Possibly Damaging	0.917	Probably Damaging	3.74	Benign	0.18	Tolerated	3.37	34	3	4	0.3	14.03
c.1972G>A	G658S (3D Viewer)	GAP				6-33441231-G-A	8	4.96e-6	-3.445	Likely Benign	0.077	Likely Benign	Likely Benign	0.070	Likely Benign	-0.12	Likely Benign	0.0	-0.50	Ambiguous	-0.31	Likely Benign	-0.11	Likely Benign	-0.97	Neutral	0.209	Benign	0.087	Benign	3.58	Benign	0.43	Tolerated	3.39	24	0	1	-0.4	30.03
c.2181C>A	N727K (3D Viewer)	GAP				6-33441646-C-A	1	6.19e-7	-10.601	Likely Pathogenic	0.884	Likely Pathogenic	Ambiguous	0.148	Likely Benign	-0.12	Likely Benign	0.2	-0.44	Likely Benign	-0.28	Likely Benign	0.86	Ambiguous	-3.82	Deleterious	0.998	Probably Damaging	0.994	Probably Damaging	2.18	Pathogenic	0.12	Tolerated	3.59	7	0	1	-0.4	14.07
c.2008C>A	L670M (3D Viewer)	GAP				6-33441267-C-A	2	1.24e-6	-9.438	Likely Pathogenic	0.125	Likely Benign	Likely Benign	0.038	Likely Benign	-0.11	Likely Benign	0.0	0.70	Ambiguous	0.30	Likely Benign	0.06	Likely Benign	-0.16	Neutral	0.970	Probably Damaging	0.777	Possibly Damaging	3.40	Benign	0.25	Tolerated	3.39	27	2	4	-1.9	18.03
c.2146C>T	R716W (3D Viewer)	GAP				6-33441611-C-T	5	3.10e-6	-11.543	Likely Pathogenic	0.766	Likely Pathogenic	Likely Benign	0.339	Likely Benign	-0.11	Likely Benign	0.0	0.87	Ambiguous	0.38	Likely Benign	0.31	Likely Benign	-6.72	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	3.32	Benign	0.00	Affected	3.50	9	-3	2	3.6	30.03
c.2033G>A	S678N (3D Viewer)	GAP				6-33441292-G-A	1	6.20e-7	-3.355	Likely Benign	0.139	Likely Benign	Likely Benign	0.067	Likely Benign	-0.10	Likely Benign	0.1	-0.47	Likely Benign	-0.29	Likely Benign	0.38	Likely Benign	-0.63	Neutral	0.001	Benign	0.002	Benign	3.43	Benign	0.14	Tolerated	3.43	19	1	1	-2.7	27.03
c.2113A>C	K705Q (3D Viewer)	GAP				6-33441372-A-C	1	6.20e-7	-5.787	Likely Benign	0.436	Ambiguous	Likely Benign	0.142	Likely Benign	-0.10	Likely Benign	0.0	0.33	Likely Benign	0.12	Likely Benign	-0.02	Likely Benign	-0.24	Neutral	0.997	Probably Damaging	0.969	Probably Damaging	3.42	Benign	0.78	Tolerated	3.47	10	1	1	0.4	-0.04
c.1120T>G	S374A (3D Viewer)	C2				6-33438025-T-G			-4.245	Likely Benign	0.082	Likely Benign	Likely Benign	0.122	Likely Benign	-0.08	Likely Benign	0.1	0.41	Likely Benign	0.17	Likely Benign	0.10	Likely Benign	-0.53	Neutral	0.012	Benign	0.011	Benign	5.32	Benign	0.04	Affected	4.32	13	1	1	2.6	-16.00
c.1520A>G	K507R (3D Viewer)	GAP				6-33438552-A-G	1	6.20e-7	-7.363	In-Between	0.085	Likely Benign	Likely Benign	0.503	Likely Pathogenic	-0.08	Likely Benign	0.1	0.38	Likely Benign	0.15	Likely Benign	0.36	Likely Benign	-0.68	Neutral	0.992	Probably Damaging	0.980	Probably Damaging	-1.48	Pathogenic	0.27	Tolerated	3.37	35	2	3	-0.6	28.01
c.1651C>A	L551M (3D Viewer)	GAP	Uncertain		1	6-33438894-C-A	7	4.34e-6	-9.937	Likely Pathogenic	0.480	Ambiguous	Likely Benign	0.544	Likely Pathogenic	-0.07	Likely Benign	0.1	0.13	Likely Benign	0.03	Likely Benign	0.71	Ambiguous	-0.56	Neutral	1.000	Probably Damaging	1.000	Probably Damaging	-1.48	Pathogenic	0.06	Tolerated	3.37	35	4	2	-1.9	18.03	246.5	-18.6	0.0	0.0	0.3	0.0						X		Potentially Benign	L551 is located on an α-helix (res. Ala533-Val560). The iso-butyl side chain of Leu551 hydrophobically packs with nearby hydrophobic residues such as Cys547, Phe652, Leu633, and Ile630 in the inter-helix space. In the variant simulations, the thioether side chain of Met551 can maintain similar hydrophobic interactions as Leu551 in the WT, thus causing no negative effect on the protein structure during the simulations.
c.1619A>G	Q540R (3D Viewer)	GAP				6-33438862-A-G	1	6.19e-7	-13.312	Likely Pathogenic	0.540	Ambiguous	Likely Benign	0.795	Likely Pathogenic	-0.06	Likely Benign	0.0	-0.07	Likely Benign	-0.07	Likely Benign	0.88	Ambiguous	-3.98	Deleterious	0.991	Probably Damaging	0.985	Probably Damaging	-1.28	Pathogenic	0.08	Tolerated	3.37	35	1	1	-1.0	28.06
c.1896C>A	N632K (3D Viewer)	GAP				6-33440948-C-A			-13.266	Likely Pathogenic	0.974	Likely Pathogenic	Likely Pathogenic	0.766	Likely Pathogenic	-0.06	Likely Benign	0.2	0.12	Likely Benign	0.03	Likely Benign	0.95	Ambiguous	-5.14	Deleterious	0.983	Probably Damaging	0.714	Possibly Damaging	-1.43	Pathogenic	0.01	Affected	3.37	34	0	1	-0.4	14.07
c.2156A>G	N719S (3D Viewer)	GAP				6-33441621-A-G	2	1.24e-6	-5.190	Likely Benign	0.072	Likely Benign	Likely Benign	0.087	Likely Benign	-0.06	Likely Benign	0.0	-0.29	Likely Benign	-0.18	Likely Benign	0.46	Likely Benign	-1.83	Neutral	0.999	Probably Damaging	0.992	Probably Damaging	2.85	Benign	0.40	Tolerated	3.50	9	1	1	2.7	-27.03
c.1556A>C	E519A (3D Viewer)	GAP	Likely Pathogenic		1				-8.557	Likely Pathogenic	0.904	Likely Pathogenic	Ambiguous	0.384	Likely Benign	-0.05	Likely Benign	0.0	0.55	Ambiguous	0.25	Likely Benign	0.00	Likely Benign	-5.23	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	3.33	Benign	0.10	Tolerated	3.37	35	0	-1	5.3	-58.04	162.4	83.5	-0.1	0.1	-0.2	0.0						X		Potentially Benign	Glu519 is located at the beginning of an α-α loop between the two α-helices (res. Gly502-Tyr518 and Ala533-Val560). In the WT simulations, the carboxylate side chain of Glu519 does not make any specific interactions. Accordingly, the Ala residue swap does not show any negative structural effects in the variant simulations. However, it should be noted that Glu519 faces the missing part of the N-terminal in the model, and thus its potential role in maintaining the tertiary structure might be de-emphasized in the current model.
c.2021C>T	T674I (3D Viewer)	GAP				6-33441280-C-T	2	1.24e-6	-8.951	Likely Pathogenic	0.521	Ambiguous	Likely Benign	0.289	Likely Benign	-0.05	Likely Benign	0.1	0.28	Likely Benign	0.12	Likely Benign	-0.04	Likely Benign	-3.18	Deleterious	0.981	Probably Damaging	0.444	Benign	3.46	Benign	0.11	Tolerated	3.40	24	-1	0	5.2	12.05
c.1067G>T	R356L (3D Viewer)	C2				6-33437972-G-T			-13.957	Likely Pathogenic	0.911	Likely Pathogenic	Ambiguous	0.412	Likely Benign	-0.04	Likely Benign	0.1	-0.57	Ambiguous	-0.31	Likely Benign	0.68	Ambiguous	-6.20	Deleterious	0.993	Probably Damaging	0.982	Probably Damaging	1.69	Pathogenic	0.02	Affected	3.39	22	-2	-3	8.3	-43.03
c.1280A>G	H427R (3D Viewer)	GAP				6-33438185-A-G			-3.259	Likely Benign	0.439	Ambiguous	Likely Benign	0.168	Likely Benign	-0.04	Likely Benign	0.1	0.48	Likely Benign	0.22	Likely Benign	0.72	Ambiguous	-2.61	Deleterious	0.174	Benign	0.018	Benign	3.51	Benign	0.03	Affected	3.38	25	0	2	-1.3	19.05
c.1300G>A	V434I (3D Viewer)	GAP	Uncertain		1	6-33438205-G-A	1	6.19e-7	-6.999	Likely Benign	0.129	Likely Benign	Likely Benign	0.192	Likely Benign	-0.04	Likely Benign	0.0	0.22	Likely Benign	0.09	Likely Benign	0.31	Likely Benign	-0.82	Neutral	0.947	Possibly Damaging	0.851	Possibly Damaging	3.53	Benign	0.18	Tolerated	3.37	29	4	3	0.3	14.03	246.7	-27.7	0.0	0.0	0.1	0.0						X		Potentially Benign	The iso-propyl side chain of Val434, located at the end of an α helix (res. Met414-Glu436), packs against hydrophobic residues in an interhelix space (e.g., Met430, Ala707, Leu711). In the variant simulations, the sec-butyl group of Ile434 is able to form the same hydrophobic interactions. Accordingly, the residue swap does not negatively affect the protein structure based on the simulations.
c.1432G>C	E478Q (3D Viewer)	GAP				6-33438464-G-C	1	6.20e-7	-9.881	Likely Pathogenic	0.603	Likely Pathogenic	Likely Benign	0.222	Likely Benign	-0.04	Likely Benign	0.0	0.31	Likely Benign	0.14	Likely Benign	0.07	Likely Benign	-2.49	Neutral	0.623	Possibly Damaging	0.199	Benign	3.40	Benign	0.14	Tolerated	3.37	34	2	2	0.0	-0.98
c.1333G>C	E445Q (3D Viewer)	GAP				6-33438238-G-C	1	6.19e-7	-12.430	Likely Pathogenic	0.790	Likely Pathogenic	Ambiguous	0.240	Likely Benign	-0.03	Likely Benign	0.0	0.20	Likely Benign	0.09	Likely Benign	0.70	Ambiguous	-2.86	Deleterious	0.987	Probably Damaging	0.946	Probably Damaging	3.40	Benign	0.12	Tolerated	3.38	31	2	2	0.0	-0.98
c.1589A>G	K530R (3D Viewer)	GAP				6-33438832-A-G	1	6.19e-7	-3.836	Likely Benign	0.081	Likely Benign	Likely Benign	0.234	Likely Benign	-0.02	Likely Benign	0.1	0.18	Likely Benign	0.08	Likely Benign	0.33	Likely Benign	-1.39	Neutral	0.000	Benign	0.002	Benign	-1.54	Pathogenic	0.08	Tolerated	3.37	35	2	3	-0.6	28.01
c.955G>C	A319P (3D Viewer)	C2				6-33437860-G-C	3	1.86e-6	-7.213	In-Between	0.109	Likely Benign	Likely Benign	0.286	Likely Benign	-0.02	Likely Benign	0.9	-1.18	Ambiguous	-0.60	Ambiguous	0.22	Likely Benign	0.11	Neutral	0.999	Probably Damaging	0.977	Probably Damaging	1.97	Pathogenic	1.00	Tolerated	3.38	23	-1	1	-3.4	26.04
c.1759A>T	R587W (3D Viewer)	GAP				6-33440811-A-T	1	6.20e-7	-15.383	Likely Pathogenic	0.878	Likely Pathogenic	Ambiguous	0.692	Likely Pathogenic	-0.01	Likely Benign	0.1	-0.44	Likely Benign	-0.23	Likely Benign	0.76	Ambiguous	-7.17	Deleterious	1.000	Probably Damaging	0.985	Probably Damaging	-1.33	Pathogenic	0.01	Affected	3.37	35	-3	2	3.6	30.03
c.1964T>A	L655Q (3D Viewer)	GAP	Uncertain		1				-5.278	Likely Benign	0.144	Likely Benign	Likely Benign	0.139	Likely Benign	-0.01	Likely Benign	0.0	0.69	Ambiguous	0.34	Likely Benign	-0.15	Likely Benign	0.61	Neutral	0.955	Possibly Damaging	0.602	Possibly Damaging	3.59	Benign	0.65	Tolerated	3.39	24	-2	-2	-7.3	14.97	229.9	-8.6	0.0	0.0	0.4	0.0						X		Potentially Benign	The iso-butyl side chain of Leu655, located on the surface of an α helix (res. Ser641-Glu666), is not involved in any interactions in the WT simulations. In the variant simulations, the carboxamide side chain of Gln655 dynamically interacts with neighboring residues (e.g., Glu651, Glu656, Arg544) on the protein surface, with no negative structural effects.
c.2147G>A	R716Q (3D Viewer)	GAP	Conflicting		2	6-33441612-G-A	4	2.48e-6	-8.338	Likely Pathogenic	0.308	Likely Benign	Likely Benign	0.210	Likely Benign	-0.01	Likely Benign	0.0	0.47	Likely Benign	0.23	Likely Benign	0.58	Ambiguous	-3.14	Deleterious	1.000	Probably Damaging	0.990	Probably Damaging	3.35	Benign	0.02	Affected	3.50	9	1	1	1.0	-28.06	250.0	48.9	0.0	0.0	-0.5	0.0						X		Uncertain	The guanidinium group of Arg716, located on the outer surface of an α-helix (res. Leu714-Arg726), forms a salt bridge with the carboxylate group of Asp720. In the variant simulations, the carboxamide group of Gln716 also forms a hydrogen bond with the carboxylate group of Asp720, although this bond is weaker than the Arg716 salt bridge in the WT. Overall, no adverse effects on the protein structure are observed in the simulations. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.1007A>G	K336R (3D Viewer)	C2				6-33437912-A-G	1	6.20e-7	-5.897	Likely Benign	0.089	Likely Benign	Likely Benign	0.038	Likely Benign	0.00	Likely Benign	0.0	-0.15	Likely Benign	-0.08	Likely Benign	0.52	Ambiguous	-2.01	Neutral	0.002	Benign	0.005	Benign	1.69	Pathogenic	0.12	Tolerated	3.38	22	2	3	-0.6	28.01
c.1165T>G	S389A (3D Viewer)	C2				6-33438070-T-G			-4.199	Likely Benign	0.081	Likely Benign	Likely Benign	0.326	Likely Benign	0.01	Likely Benign	0.0	0.37	Likely Benign	0.19	Likely Benign	0.03	Likely Benign	-0.39	Neutral	0.140	Benign	0.355	Benign	5.08	Benign	0.04	Affected	4.32	8	1	1	2.6	-16.00
c.2158G>A	D720N (3D Viewer)	GAP	Likely Benign		1	6-33441623-G-A	5	3.10e-6	-9.135	Likely Pathogenic	0.654	Likely Pathogenic	Likely Benign	0.289	Likely Benign	0.01	Likely Benign	0.0	-0.20	Likely Benign	-0.10	Likely Benign	0.46	Likely Benign	-3.74	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	2.18	Pathogenic	0.01	Affected	3.50	9	1	2	0.0	-0.98
c.836G>T	R279L (3D Viewer)	C2				6-33437741-G-T	1	6.20e-7	-12.390	Likely Pathogenic	0.926	Likely Pathogenic	Ambiguous	0.576	Likely Pathogenic	0.01	Likely Benign	0.2	0.14	Likely Benign	0.08	Likely Benign	0.39	Likely Benign	-5.37	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	1.91	Pathogenic	0.03	Affected	3.39	18	-2	-3	8.3	-43.03
c.1449A>G	I483M (3D Viewer)	GAP				6-33438481-A-G	1	6.20e-7	-8.839	Likely Pathogenic	0.777	Likely Pathogenic	Likely Benign	0.261	Likely Benign	0.02	Likely Benign	0.0	0.73	Ambiguous	0.38	Likely Benign	1.06	Destabilizing	-2.78	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.26	Benign	0.05	Affected	3.37	32	1	2	-2.6	18.03
c.1852C>A	Q618K (3D Viewer)	GAP				6-33440904-C-A	24	1.49e-5	-7.708	In-Between	0.229	Likely Benign	Likely Benign	0.281	Likely Benign	0.02	Likely Benign	0.0	0.16	Likely Benign	0.09	Likely Benign	-0.46	Likely Benign	-0.05	Neutral	0.338	Benign	0.111	Benign	-1.21	Pathogenic	0.29	Tolerated	3.37	35	1	1	-0.4	0.04
c.1153T>G	S385A (3D Viewer)	C2				6-33438058-T-G			-4.412	Likely Benign	0.083	Likely Benign	Likely Benign	0.243	Likely Benign	0.03	Likely Benign	0.1	0.19	Likely Benign	0.11	Likely Benign	0.07	Likely Benign	-0.28	Neutral	0.140	Benign	0.355	Benign	4.65	Benign	0.13	Tolerated	4.32	3	1	1	2.6	-16.00
c.829A>C	K277Q (3D Viewer)	C2				6-33437734-A-C	1	6.20e-7	-12.547	Likely Pathogenic	0.904	Likely Pathogenic	Ambiguous	0.655	Likely Pathogenic	0.03	Likely Benign	0.1	0.63	Ambiguous	0.33	Likely Benign	0.42	Likely Benign	-3.68	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.83	Pathogenic	0.02	Affected	3.38	19	1	1	0.4	-0.04
c.1166C>T	S389L (3D Viewer)	C2				6-33438071-C-T	7	4.40e-6	-6.040	Likely Benign	0.165	Likely Benign	Likely Benign	0.456	Likely Benign	0.04	Likely Benign	0.1	0.69	Ambiguous	0.37	Likely Benign	-0.23	Likely Benign	-0.75	Neutral	0.462	Possibly Damaging	0.693	Possibly Damaging	5.05	Benign	0.01	Affected	4.32	8	-2	-3	4.6	26.08
c.1349C>T	A450V (3D Viewer)	GAP				6-33438254-C-T	1	6.20e-7	-11.489	Likely Pathogenic	0.578	Likely Pathogenic	Likely Benign	0.306	Likely Benign	0.04	Likely Benign	0.2	0.27	Likely Benign	0.16	Likely Benign	0.46	Likely Benign	-3.69	Deleterious	0.998	Probably Damaging	0.955	Probably Damaging	3.55	Benign	0.04	Affected	3.37	32	0	0	2.4	28.05
c.2120C>T	A707V (3D Viewer)	GAP				6-33441585-C-T	1	6.20e-7	-6.479	Likely Benign	0.277	Likely Benign	Likely Benign	0.212	Likely Benign	0.05	Likely Benign	0.0	2.17	Destabilizing	1.11	Ambiguous	-0.30	Likely Benign	-1.62	Neutral	0.991	Probably Damaging	0.912	Probably Damaging	3.45	Benign	1.00	Tolerated	3.50	9	0	0	2.4	28.05
c.1456G>A	E486K (3D Viewer)	GAP	Uncertain		1				-14.545	Likely Pathogenic	0.988	Likely Pathogenic	Likely Pathogenic	0.435	Likely Benign	0.06	Likely Benign	0.1	0.37	Likely Benign	0.22	Likely Benign	0.41	Likely Benign	-3.58	Deleterious	1.000	Probably Damaging	0.988	Probably Damaging	3.40	Benign	0.12	Tolerated	3.37	35	0	1	-0.4	-0.94	206.8	52.1	-0.3	0.1	0.2	0.0	X			X				Uncertain	Glu486 is located in an α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. It is adjacent to the arginine finger (Arg485) and is expected to closely interact with Ras. The residue swap could affect complex formation with the GTPase and its activation. In the WT simulations, the carboxylate group of Glu486 forms salt bridges with Arg485 and Arg475 on the preceding α-helix (res. Ala461-Phe476). In the variant simulations, Lys486 does not form any specific interactions. Although the amino group of the Lys486 side chain cannot form these salt bridges, no negative effects on the protein structure are observed. Nevertheless, the potential role of Glu486 in SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations, and no definite conclusions can be drawn.
c.1180A>G	K394E (3D Viewer)	C2				6-33438085-A-G	1	6.20e-7	-6.903	Likely Benign	0.896	Likely Pathogenic	Ambiguous	0.446	Likely Benign	0.07	Likely Benign	0.1	3.71	Destabilizing	1.89	Ambiguous	1.20	Destabilizing	-2.54	Deleterious	0.063	Benign	0.038	Benign	4.61	Benign	0.04	Affected	3.44	14	1	0	0.4	0.94
c.1576G>A	V526I (3D Viewer)	GAP				6-33438819-G-A			-9.962	Likely Pathogenic	0.526	Ambiguous	Likely Benign	0.540	Likely Pathogenic	0.07	Likely Benign	0.3	0.41	Likely Benign	0.24	Likely Benign	0.02	Likely Benign	-0.99	Neutral	0.929	Possibly Damaging	0.917	Probably Damaging	-1.34	Pathogenic	0.15	Tolerated	3.37	35	3	4	0.3	14.03
c.1913A>G	K638R (3D Viewer)	GAP	Uncertain		1				-2.700	Likely Benign	0.110	Likely Benign	Likely Benign	0.216	Likely Benign	0.09	Likely Benign	0.1	-0.04	Likely Benign	0.03	Likely Benign	0.53	Ambiguous	-2.55	Deleterious	0.649	Possibly Damaging	0.240	Benign	3.41	Benign	0.13	Tolerated	3.37	31	2	3	-0.6	28.01
c.686A>G	K229R (3D Viewer)	PH				6-33435537-A-G	1	6.20e-7	-5.651	Likely Benign	0.436	Ambiguous	Likely Benign	0.628	Likely Pathogenic	0.09	Likely Benign	0.0	0.02	Likely Benign	0.06	Likely Benign	0.40	Likely Benign	-2.00	Neutral	0.993	Probably Damaging	0.971	Probably Damaging	5.84	Benign	0.19	Tolerated	3.43	12	2	3	-0.6	28.01
c.1121C>G	S374C (3D Viewer)	C2				6-33438026-C-G			-6.242	Likely Benign	0.106	Likely Benign	Likely Benign	0.317	Likely Benign	0.10	Likely Benign	0.0	0.79	Ambiguous	0.45	Likely Benign	0.08	Likely Benign	-0.99	Neutral	0.875	Possibly Damaging	0.430	Benign	5.30	Benign	0.00	Affected	4.32	13	-1	0	3.3	16.06
c.1471A>G	T491A (3D Viewer)	GAP				6-33438503-A-G	1	6.20e-7	-11.033	Likely Pathogenic	0.933	Likely Pathogenic	Ambiguous	0.851	Likely Pathogenic	0.10	Likely Benign	0.3	-0.27	Likely Benign	-0.09	Likely Benign	1.06	Destabilizing	-4.82	Deleterious	0.998	Probably Damaging	0.989	Probably Damaging	-1.47	Pathogenic	0.01	Affected	3.37	35	0	1	2.5	-30.03
c.1752C>G	I584M (3D Viewer)	GAP	Uncertain		2	6-33440804-C-G	1	6.20e-7	-10.119	Likely Pathogenic	0.419	Ambiguous	Likely Benign	0.478	Likely Benign	0.11	Likely Benign	0.1	0.46	Likely Benign	0.29	Likely Benign	1.16	Destabilizing	-2.62	Deleterious	0.983	Probably Damaging	0.925	Probably Damaging	-1.25	Pathogenic	0.12	Tolerated	3.37	34	2	1	-2.6	18.03	247.5	-20.3	-0.1	0.3	-0.1	0.1						X		Potentially Benign	A hydrophobic residue, Ile584, located in an α helix (res. Glu582-Met603), is swapped for another hydrophobic residue, Met584. The sec-butyl hydrocarbon side chain of Ile584 packs hydrophobically with residues in an inter-helix hydrophobic space (e.g., Leu588, Met477, Val473, and Ile483).In the variant simulations, the thioether hydrophobic side chain of Met584 maintains similar interactions as Ile584 in the WT, as it is roughly the same size and fits well within the hydrophobic space. Thus, the residue swap does not appear to cause any negative effects on the protein structure.
c.1851G>T	E617D (3D Viewer)	GAP	Uncertain		1				-1.349	Likely Benign	0.241	Likely Benign	Likely Benign	0.322	Likely Benign	0.12	Likely Benign	0.1	0.80	Ambiguous	0.46	Likely Benign	0.07	Likely Benign	-0.01	Neutral	0.994	Probably Damaging	0.979	Probably Damaging	-1.35	Pathogenic	0.88	Tolerated	3.37	35	2	3	0.0	-14.03
c.804C>G	I268M (3D Viewer)	C2				6-33437709-C-G	1	6.20e-7	-9.721	Likely Pathogenic	0.739	Likely Pathogenic	Likely Benign	0.622	Likely Pathogenic	0.12	Likely Benign	0.2	0.95	Ambiguous	0.54	Ambiguous	1.32	Destabilizing	-2.58	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	1.52	Pathogenic	0.01	Affected	3.38	19	1	2	-2.6	18.03
c.1129A>C	M377L (3D Viewer)	C2				6-33438034-A-C	1	1.95e-6	-2.394	Likely Benign	0.082	Likely Benign	Likely Benign	0.175	Likely Benign	0.13	Likely Benign	0.1	0.69	Ambiguous	0.41	Likely Benign	0.16	Likely Benign	-0.32	Neutral	0.000	Benign	0.001	Benign	5.46	Benign	0.58	Tolerated	4.32	12	2	4	1.9	-18.03
c.1129A>T	M377L (3D Viewer)	C2				6-33438034-A-T			-2.394	Likely Benign	0.082	Likely Benign	Likely Benign	0.186	Likely Benign	0.13	Likely Benign	0.1	0.69	Ambiguous	0.41	Likely Benign	0.16	Likely Benign	-0.32	Neutral	0.000	Benign	0.001	Benign	5.46	Benign	0.58	Tolerated	4.32	12	2	4	1.9	-18.03
c.1325A>G	K442R (3D Viewer)	GAP				6-33438230-A-G	1	6.20e-7	-5.761	Likely Benign	0.093	Likely Benign	Likely Benign	0.098	Likely Benign	0.13	Likely Benign	0.1	0.29	Likely Benign	0.21	Likely Benign	0.51	Ambiguous	-1.42	Neutral	0.972	Probably Damaging	0.875	Possibly Damaging	3.46	Benign	0.35	Tolerated	3.37	29	2	3	-0.6	28.01
c.1385A>G	K462R (3D Viewer)	GAP				6-33438290-A-G	1	6.20e-7	-9.980	Likely Pathogenic	0.184	Likely Benign	Likely Benign	0.246	Likely Benign	0.13	Likely Benign	0.1	0.90	Ambiguous	0.52	Ambiguous	0.84	Ambiguous	-2.75	Deleterious	0.983	Probably Damaging	0.962	Probably Damaging	3.43	Benign	0.09	Tolerated	3.37	34	2	3	-0.6	28.01
c.1511A>G	K504R (3D Viewer)	GAP	Uncertain		1	6-33438543-A-G	2	1.24e-6	-4.365	Likely Benign	0.088	Likely Benign	Likely Benign	0.238	Likely Benign	0.13	Likely Benign	0.1	0.51	Ambiguous	0.32	Likely Benign	0.94	Ambiguous	-2.16	Neutral	0.002	Benign	0.015	Benign	-1.41	Pathogenic	0.11	Tolerated	3.37	35	2	3	-0.6	28.01
c.1747G>A	D583N (3D Viewer)	GAP				6-33440799-G-A	3	1.86e-6	-8.048	Likely Pathogenic	0.856	Likely Pathogenic	Ambiguous	0.632	Likely Pathogenic	0.13	Likely Benign	0.1	0.00	Likely Benign	0.07	Likely Benign	0.21	Likely Benign	-4.78	Deleterious	0.996	Probably Damaging	0.995	Probably Damaging	-1.40	Pathogenic	0.09	Tolerated	3.37	35	1	2	0.0	-0.98
c.1970G>T	W657L (3D Viewer)	GAP	Uncertain		1				-14.411	Likely Pathogenic	0.960	Likely Pathogenic	Likely Pathogenic	0.213	Likely Benign	0.14	Likely Benign	0.1	0.73	Ambiguous	0.44	Likely Benign	0.87	Ambiguous	-10.86	Deleterious	0.277	Benign	0.078	Benign	3.52	Benign	0.14	Tolerated	3.39	24	-2	-2	4.7	-73.05
c.2186A>G	N729S (3D Viewer)	GAP	Uncertain		1				-1.578	Likely Benign	0.066	Likely Benign	Likely Benign	0.063	Likely Benign	0.14	Likely Benign	0.1	1.34	Ambiguous	0.74	Ambiguous	-0.36	Likely Benign	-0.42	Neutral	0.221	Benign	0.027	Benign	3.38	Benign	0.93	Tolerated	3.59	7	1	1	2.7	-27.03
c.773G>T	R258L (3D Viewer)	C2				6-33437678-G-T	1	6.20e-7	-13.302	Likely Pathogenic	0.905	Likely Pathogenic	Ambiguous	0.908	Likely Pathogenic	0.14	Likely Benign	0.2	0.10	Likely Benign	0.12	Likely Benign	0.52	Ambiguous	-5.90	Deleterious	0.997	Probably Damaging	0.987	Probably Damaging	5.84	Benign	0.01	Affected	3.39	15	-2	-3	8.3	-43.03
c.1018G>T	A340S (3D Viewer)	C2				6-33437923-G-T	1	6.20e-7	-0.705	Likely Benign	0.083	Likely Benign	Likely Benign	0.083	Likely Benign	0.15	Likely Benign	0.0	0.27	Likely Benign	0.21	Likely Benign	-0.46	Likely Benign	1.62	Neutral	0.007	Benign	0.008	Benign	1.93	Pathogenic	0.51	Tolerated	3.42	13	1	1	-2.6	16.00
c.1483G>A	E495K (3D Viewer)	GAP	Uncertain		1				-11.478	Likely Pathogenic	0.986	Likely Pathogenic	Likely Pathogenic	0.869	Likely Pathogenic	0.15	Likely Benign	0.2	0.66	Ambiguous	0.41	Likely Benign	0.70	Ambiguous	-3.91	Deleterious	0.999	Probably Damaging	0.994	Probably Damaging	-1.29	Pathogenic	0.01	Affected	3.37	35	1	0	-0.4	-0.94
c.1154C>T	S385L (3D Viewer)	C2	Uncertain		1	6-33438059-C-T	9	4.60e-5	-6.018	Likely Benign	0.167	Likely Benign	Likely Benign	0.304	Likely Benign	0.16	Likely Benign	0.1	0.08	Likely Benign	0.12	Likely Benign	-0.26	Likely Benign	-0.68	Neutral	0.829	Possibly Damaging	0.706	Possibly Damaging	4.63	Benign	0.01	Affected	4.32	3	-3	-2	4.6	26.08	244.6	-50.1	0.0	0.6	-0.1	0.1								Uncertain	Ser385 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like leucine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Leu385 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effects on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.2030G>A	S677N (3D Viewer)	GAP				6-33441289-G-A	1	6.20e-7	-7.955	In-Between	0.111	Likely Benign	Likely Benign	0.079	Likely Benign	0.17	Likely Benign	0.5	-0.15	Likely Benign	0.01	Likely Benign	0.89	Ambiguous	-2.05	Neutral	0.038	Benign	0.007	Benign	3.28	Benign	0.15	Tolerated	3.41	23	1	1	-2.7	27.03
c.1585A>G	I529V (3D Viewer)	GAP				6-33438828-A-G	1	6.20e-7	-2.342	Likely Benign	0.068	Likely Benign	Likely Benign	0.230	Likely Benign	0.18	Likely Benign	0.0	0.03	Likely Benign	0.11	Likely Benign	0.36	Likely Benign	-0.21	Neutral	0.019	Benign	0.014	Benign	-1.24	Pathogenic	1.00	Tolerated	3.37	35	3	4	-0.3	-14.03
c.2011G>A	D671N (3D Viewer)	GAP				6-33441270-G-A			-10.347	Likely Pathogenic	0.685	Likely Pathogenic	Likely Benign	0.184	Likely Benign	0.18	Likely Benign	0.1	0.39	Likely Benign	0.29	Likely Benign	0.19	Likely Benign	-3.19	Deleterious	0.887	Possibly Damaging	0.592	Possibly Damaging	3.36	Benign	0.02	Affected	3.39	27	1	2	0.0	-0.98
c.1370G>A	S457N	GAP	Uncertain		1				-10.221	Likely Pathogenic	0.949	Likely Pathogenic	Ambiguous	0.241	Likely Benign	0.19	Likely Benign	0.0	-0.22	Likely Benign	-0.02	Likely Benign	0.67	Ambiguous	-2.76	Deleterious	0.940	Possibly Damaging	0.843	Possibly Damaging	3.28	Benign	0.06	Tolerated			1	1	-2.7	27.03
c.1631G>A	R544Q (3D Viewer)	GAP	Uncertain		1	6-33438874-G-A	1	6.20e-7	-10.281	Likely Pathogenic	0.596	Likely Pathogenic	Likely Benign	0.542	Likely Pathogenic	0.19	Likely Benign	0.2	0.87	Ambiguous	0.53	Ambiguous	1.40	Destabilizing	-2.41	Neutral	1.000	Probably Damaging	0.997	Probably Damaging	-1.40	Pathogenic	0.09	Tolerated	3.37	35	1	1	1.0	-28.06
c.1055C>A	T352N (3D Viewer)	C2	Likely Benign		1	6-33437960-C-A	2	1.24e-6	-4.817	Likely Benign	0.117	Likely Benign	Likely Benign	0.027	Likely Benign	0.20	Likely Benign	0.0	-0.04	Likely Benign	0.08	Likely Benign	0.45	Likely Benign	-0.92	Neutral	0.255	Benign	0.057	Benign	1.75	Pathogenic	0.19	Tolerated	3.37	25	0	0	-2.8	13.00	208.4	-14.5	-0.2	0.1	-0.1	0.0		X						Potentially Benign	Thr352 is located in a short α helical section within a loop connecting two β strands (res. Gly341-Pro349, res. Thr359-Pro364) originating from two different anti-parallel β sheets of the C2 domain. In the WT simulations, the side chain hydroxyl and backbone amide groups of Thr354 form hydrogen bonds with the backbone carbonyl group of Pro349 at the end of the preceding β strand. This arrangement likely stabilizes the α helical section and aids in folding, keeping the short secondary structure element intact in the variant simulations. However, the carboxamide group of the Asn352 side chain does not form hydrogen bonds with the backbone carbonyl group of Pro349. Instead, it packs against the cyclic ring and forms hydrogen bonds with the phenol group of the Tyr363 side chain in the other β strand.
c.2015C>A	T672K (3D Viewer)	GAP	Uncertain		1				-12.192	Likely Pathogenic	0.698	Likely Pathogenic	Likely Benign	0.065	Likely Benign	0.20	Likely Benign	0.5	1.21	Ambiguous	0.71	Ambiguous	0.72	Ambiguous	-4.31	Deleterious	0.745	Possibly Damaging	0.051	Benign	3.40	Benign	0.07	Tolerated	3.40	25	0	-1	-3.2	27.07	195.1	7.0	0.4	0.7	0.4	0.1		X				X		Potentially Pathogenic	The hydroxyl group of Thr672, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop itself, such as Lys566, Glu666, and Asn669. In the variant simulations, Lys672 can only form a hydrogen bond with the amino group of the Lys566 side chain via its backbone carbonyl group. Consequently, it cannot maintain the Lys566-Glu666 salt bridge through hydrogen bonding. However, the amino group of Lys periodically forms a salt bridge with the carboxylate group of Glu666, which prevents a drastic disruption of the hydrogen-bond network that keeps the loop close to the helices.
c.1312G>A	A438T (3D Viewer)	GAP	Uncertain		3	6-33438217-G-A	16	9.91e-6	-5.339	Likely Benign	0.085	Likely Benign	Likely Benign	0.021	Likely Benign	0.21	Likely Benign	0.0	-0.07	Likely Benign	0.07	Likely Benign	0.36	Likely Benign	-0.81	Neutral	0.300	Benign	0.011	Benign	4.18	Benign	0.14	Tolerated	3.38	26	1	0	-2.5	30.03	214.2	-42.7	-0.3	0.1	-0.4	0.1						X		Potentially Benign	The methyl group of Ala438, located in a four-residue loop connecting two α helices (res. Asn440-Thr458 and Pro413-Glu436), packs against hydrophobic residues from a nearby α helix or loop residues (e.g., Leu703, Val699). In the variant simulations, the methyl group of Thr438 is able to establish similar hydrophobic packing. Moreover, the hydroxyl group also H-bonds with nearby residues, such as the carbonyl group of the neighboring loop residue Pro437. Accordingly, the residue swap does not generate an apparent negative effect on the protein structure based on the simulations.
c.701G>A	R234Q (3D Viewer)	PH				6-33435552-G-A	8	4.96e-6	-9.675	Likely Pathogenic	0.666	Likely Pathogenic	Likely Benign	0.627	Likely Pathogenic	0.21	Likely Benign	0.1	0.27	Likely Benign	0.24	Likely Benign	0.57	Ambiguous	-2.32	Neutral	0.892	Possibly Damaging	0.213	Benign	5.81	Benign	0.11	Tolerated	3.40	14	1	1	1.0	-28.06
c.884C>T	T295I (3D Viewer)	C2				6-33437789-C-T	4	2.48e-6	-9.330	Likely Pathogenic	0.892	Likely Pathogenic	Ambiguous	0.607	Likely Pathogenic	0.21	Likely Benign	0.2	0.55	Ambiguous	0.38	Likely Benign	0.58	Ambiguous	-4.87	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.88	Pathogenic	0.04	Affected	3.38	23	-1	0	5.2	12.05
c.859G>T	D287Y (3D Viewer)	C2	Likely Pathogenic		1				-12.877	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.663	Likely Pathogenic	0.21	Likely Benign	0.2	0.48	Likely Benign	0.35	Likely Benign	0.27	Likely Benign	-8.27	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.51	Pathogenic	0.00	Affected	3.38	23	-4	-3	2.2	48.09	257.8	-44.4	-0.6	1.6	0.2	0.3	X	X						Potentially Pathogenic	The carboxylate group of Asp287, located at the beginning of a β hairpin loop linking two anti-parallel β sheet strands (res. Arg279-Leu286, res. Met289-Pro298), maintains a salt bridge with the guanidinium group of Arg324 in the β sheet during the WT simulations. In the variant simulations, the phenol group of the Tyr287 side chain is unable to form a salt bridge with the guanidinium group of Arg324, which could weaken the tertiary structure assembly of the C2 domain. However, the phenol group of Tyr287 frequently stacks with the Arg324 guanidinium side chain, which could help maintain the tertiary structure, especially compared to the D287H variant. The destabilization of the C2 domain could adversely affect the stability of the SynGAP-membrane association.
c.1586T>C	I529T (3D Viewer)	GAP	Uncertain		1				-0.539	Likely Benign	0.336	Likely Benign	Likely Benign	0.343	Likely Benign	0.22	Likely Benign	0.2	0.16	Likely Benign	0.19	Likely Benign	0.17	Likely Benign	0.24	Neutral	0.872	Possibly Damaging	0.820	Possibly Damaging	-1.23	Pathogenic	0.55	Tolerated	3.37	35	0	-1	-5.2	-12.05	207.2	29.8	0.2	0.0	0.2	0.1						X		Potentially Benign	Ile529 is located on an α-α loop between the two α-helices (res. Gly502-Tyr518 and Ala533-Val560). In the WT simulations, the sec-butyl side chain of Ile529 faces the membrane interface and shows no specific interactions. In the variant simulations, the hydroxyl group of Thr529 forms a hydrogen bond with the carboxylate side chain of Asp527, but no negative structural changes are observed. However, due to its location near the SynGAP-membrane interface, the effect of the residue swap cannot be fully addressed using the SynGAP solvent-only simulations.
c.1883A>G	K628R (3D Viewer)	GAP				6-33440935-A-G	1	6.20e-7	-11.324	Likely Pathogenic	0.476	Ambiguous	Likely Benign	0.592	Likely Pathogenic	0.22	Likely Benign	0.1	-0.11	Likely Benign	0.06	Likely Benign	0.94	Ambiguous	-2.99	Deleterious	0.996	Probably Damaging	0.990	Probably Damaging	2.49	Pathogenic	0.00	Affected	3.37	34	2	3	-0.6	28.01
c.718G>A	D240N		Uncertain		1				-12.942	Likely Pathogenic	0.755	Likely Pathogenic	Likely Benign	0.701	Likely Pathogenic	0.22	Likely Benign	0.9	0.47	Likely Benign	0.35	Likely Benign	0.37	Likely Benign	-4.37	Deleterious	0.993	Probably Damaging	0.984	Probably Damaging	5.88	Benign	0.01	Affected			2	1	0.0	-0.98
c.1819C>T	L607F (3D Viewer)	GAP				6-33440871-C-T	1	6.19e-7	-13.654	Likely Pathogenic	0.948	Likely Pathogenic	Ambiguous	0.758	Likely Pathogenic	0.23	Likely Benign	0.1	1.20	Ambiguous	0.72	Ambiguous	0.61	Ambiguous	-3.98	Deleterious	0.998	Probably Damaging	0.997	Probably Damaging	-1.54	Pathogenic	0.01	Affected	3.37	35	0	2	-1.0	34.02
c.2164A>G	S722G (3D Viewer)	GAP				6-33441629-A-G	2	1.24e-6	-9.141	Likely Pathogenic	0.214	Likely Benign	Likely Benign	0.270	Likely Benign	0.24	Likely Benign	0.1	0.67	Ambiguous	0.46	Likely Benign	0.50	Likely Benign	-2.72	Deleterious	0.998	Probably Damaging	0.863	Possibly Damaging	2.49	Pathogenic	0.14	Tolerated	3.50	8	0	1	0.4	-30.03
c.651G>T	E217D (3D Viewer)	PH				6-33435293-G-T	1	6.20e-7	-2.268	Likely Benign	0.453	Ambiguous	Likely Benign	0.276	Likely Benign	0.24	Likely Benign	0.3	-0.07	Likely Benign	0.09	Likely Benign	-0.34	Likely Benign	0.66	Neutral	0.014	Benign	0.007	Benign	5.85	Benign	0.85	Tolerated	3.41	13	2	3	0.0	-14.03
c.649G>C	E217Q (3D Viewer)	PH				6-33435291-G-C	1	6.20e-7	-6.810	Likely Benign	0.949	Likely Pathogenic	Ambiguous	0.459	Likely Benign	0.25	Likely Benign	0.2	1.61	Ambiguous	0.93	Ambiguous	0.67	Ambiguous	-1.89	Neutral	0.900	Possibly Damaging	0.461	Possibly Damaging	5.83	Benign	0.14	Tolerated	3.41	13	2	2	0.0	-0.98
c.667A>T	T223S (3D Viewer)	PH	Benign		1	6-33435518-A-T	3	1.86e-6	-7.714	In-Between	0.410	Ambiguous	Likely Benign	0.535	Likely Pathogenic	0.26	Likely Benign	0.1	0.50	Ambiguous	0.38	Likely Benign	0.62	Ambiguous	-2.86	Deleterious	0.421	Benign	0.058	Benign	5.80	Benign	0.02	Affected	3.41	13	1	1	-0.1	-14.03	200.7	17.3	-0.2	0.2	0.0	0.0						X		Uncertain	The introduced residue Ser223 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Its hydroxyl group forms hydrogen bonds with nearby residues Thr228 and Lys207 in the variant simulations, similar to the hydroxyl group of Thr223 in the WT simulations. These hydrogen-bonding interactions at the β sheet surface contribute to the stability of the secondary structure element and may prevent it from unfolding. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.819G>T	E273D (3D Viewer)	C2	Benign		1	6-33437724-G-T	2	1.24e-6	-1.811	Likely Benign	0.058	Likely Benign	Likely Benign	0.092	Likely Benign	0.26	Likely Benign	0.1	-0.48	Likely Benign	-0.11	Likely Benign	-0.63	Ambiguous	1.99	Neutral	0.004	Benign	0.010	Benign	2.00	Pathogenic	1.00	Tolerated	3.38	18	3	2	0.0	-14.03	223.1	22.1	0.2	0.0	0.0	0.1						X		Potentially Benign	The negatively charged residue Glu273, located in a β hairpin loop (res. Glu273-Lys278) that connects two anti-parallel β sheet strands, is replaced with another negatively charged residue, aspartate. Because the C2 domain loop faces the membrane surface, the potentially crucial role of the carboxylate group of Glu273 or Asp273 on SynGAP-membrane association cannot be fully explored via solvent-only simulations.As a minor note, the neighboring residue Arg272, which stacks with the indole ring of the Trp362 side chain and directly faces RasGTPase, forms a salt bridge more often with Asp273 than with the non-mutated Glu273 in the simulations. Regardless, due to the similar physicochemical properties of the WT and variant residues at the membrane interface, the residue swap is likely to be well tolerated.
c.1078G>A	E360K (3D Viewer)	C2				6-33437983-G-A			-16.006	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.526	Likely Pathogenic	0.27	Likely Benign	0.0	2.21	Destabilizing	1.24	Ambiguous	0.55	Ambiguous	-3.68	Deleterious	0.997	Probably Damaging	0.980	Probably Damaging	1.68	Pathogenic	0.04	Affected	3.37	25	1	0	-0.4	-0.94
c.784A>G	N262D (3D Viewer)	C2				6-33437689-A-G	1	6.20e-7	-13.363	Likely Pathogenic	0.848	Likely Pathogenic	Ambiguous	0.820	Likely Pathogenic	0.27	Likely Benign	0.1	0.36	Likely Benign	0.32	Likely Benign	1.16	Destabilizing	-4.31	Deleterious	0.997	Probably Damaging	0.980	Probably Damaging	5.85	Benign	0.05	Affected	3.40	14	1	2	0.0	0.98
c.1022G>A	G341D (3D Viewer)	C2				6-33437927-G-A	6	3.72e-6	-7.402	In-Between	0.871	Likely Pathogenic	Ambiguous	0.295	Likely Benign	0.28	Likely Benign	0.1	-1.32	Ambiguous	-0.52	Ambiguous	-0.04	Likely Benign	-0.11	Neutral	0.454	Possibly Damaging	0.192	Benign	0.34	Pathogenic	0.25	Tolerated	3.42	13	-1	1	-3.1	58.04
c.1609G>T	A537S (3D Viewer)	GAP				6-33438852-G-T	1	6.20e-7	-3.602	Likely Benign	0.095	Likely Benign	Likely Benign	0.206	Likely Benign	0.28	Likely Benign	0.0	0.46	Likely Benign	0.37	Likely Benign	0.28	Likely Benign	-0.66	Neutral	0.528	Possibly Damaging	0.592	Possibly Damaging	-1.25	Pathogenic	0.60	Tolerated	3.37	35	1	1	-2.6	16.00
c.1742G>T	R581L (3D Viewer)	GAP				6-33440794-G-T	3	1.86e-6	-10.134	Likely Pathogenic	0.958	Likely Pathogenic	Likely Pathogenic	0.654	Likely Pathogenic	0.29	Likely Benign	0.1	-0.20	Likely Benign	0.05	Likely Benign	0.45	Likely Benign	-5.93	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.33	Pathogenic	0.08	Tolerated	3.37	34	-2	-3	8.3	-43.03
c.674C>T	S225L (3D Viewer)	PH				6-33435525-C-T	1	6.20e-7	-6.644	Likely Benign	0.103	Likely Benign	Likely Benign	0.320	Likely Benign	0.29	Likely Benign	0.4	1.18	Ambiguous	0.74	Ambiguous	0.18	Likely Benign	-3.76	Deleterious	0.000	Benign	0.001	Benign	5.70	Benign	0.28	Tolerated	3.41	13	-2	-3	4.6	26.08
c.1597G>A	A533T (3D Viewer)	GAP				6-33438840-G-A	2	1.24e-6	-5.396	Likely Benign	0.084	Likely Benign	Likely Benign	0.147	Likely Benign	0.30	Likely Benign	0.1	0.31	Likely Benign	0.31	Likely Benign	0.19	Likely Benign	-0.48	Neutral	0.002	Benign	0.001	Benign	-1.26	Pathogenic	0.11	Tolerated	3.37	35	0	1	-2.5	30.03
c.667A>G	T223A (3D Viewer)	PH	Uncertain		1	6-33435518-A-G	3	1.86e-6	-7.076	In-Between	0.316	Likely Benign	Likely Benign	0.574	Likely Pathogenic	0.30	Likely Benign	0.1	0.77	Ambiguous	0.54	Ambiguous	0.74	Ambiguous	-3.36	Deleterious	0.231	Benign	0.058	Benign	5.74	Benign	0.09	Tolerated	3.41	13	1	0	2.5	-30.03	186.4	44.0	0.0	0.0	0.0	0.0	X	X						Uncertain	The introduced residue Ala223 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Unlike the hydroxyl group of the Thr223 side chain in the WT protein, the methyl side chain of Ala223 cannot form hydrogen bonds with nearby residues Thr228 and Lys207. Without these hydrogen-bonding interactions at the β sheet surface, the secondary structure element becomes unstable and partially unfolds in the variant simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.860A>C	D287A (3D Viewer)	C2	Uncertain		1				-14.686	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.484	Likely Benign	0.30	Likely Benign	0.1	-0.04	Likely Benign	0.13	Likely Benign	0.40	Likely Benign	-7.35	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.58	Pathogenic	0.01	Affected	3.38	23	-2	0	5.3	-44.01
c.910G>A	D304N (3D Viewer)	C2	Uncertain		1				-6.194	Likely Benign	0.391	Ambiguous	Likely Benign	0.345	Likely Benign	0.30	Likely Benign	0.1	-0.08	Likely Benign	0.11	Likely Benign	0.21	Likely Benign	-4.18	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	1.81	Pathogenic	0.03	Affected	3.38	23	1	2	0.0	-0.98
c.1285C>T	R429W (3D Viewer)	GAP	Conflicting		5	6-33438190-C-T	65	4.03e-5	-10.666	Likely Pathogenic	0.500	Ambiguous	Likely Benign	0.282	Likely Benign	0.31	Likely Benign	0.1	-0.13	Likely Benign	0.09	Likely Benign	0.52	Ambiguous	-3.19	Deleterious	1.000	Probably Damaging	0.990	Probably Damaging	3.41	Benign	0.03	Affected	3.38	25	2	-3	3.6	30.03	252.3	45.5	0.0	0.0	0.2	0.1		X						Potentially Pathogenic	The guanidinium group of Arg429, located in an α helix (res. Met414-Glu436), either forms a salt bridge with the carboxylate group of an acidic residue (Asp474, Asp467) or a H-bond with the hydroxyl group of Ser471 in an opposing α helix (res. Ala461-Phe476). In the variant simulations, the indole ring of the Trp429 side chain cannot form ionic interactions with the acidic residues. Although it forms a H-bond with Ser471, the bonding is not as strong as that of arginine. The residue swap could affect the tertiary structure assembly during folding; however, no large-scale negative effects were seen during the simulations.
c.2015C>T	T672M (3D Viewer)	GAP	Conflicting		2	6-33441274-C-T	19	1.18e-5	-9.472	Likely Pathogenic	0.174	Likely Benign	Likely Benign	0.127	Likely Benign	0.31	Likely Benign	0.4	1.52	Ambiguous	0.92	Ambiguous	0.41	Likely Benign	-4.34	Deleterious	0.993	Probably Damaging	0.520	Possibly Damaging	3.39	Benign	0.00	Affected	3.40	25	-1	-1	2.6	30.09	231.9	-52.9	1.1	0.1	0.5	0.0		X				X		Potentially Pathogenic	The hydroxyl group of Thr672, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop itself, such as Lys566, Glu666, and Asn669. Met672 can only form a hydrogen bond with the amino group of the Lys566 side chain via its backbone carbonyl group. Nevertheless, the Lys566-Glu666 salt bridge forms intermittently. This is possible because Asn669 keeps the carboxylate group of Glu666 in the vicinity through hydrogen bonding, and the hydrophobic side chain of Met stays mostly rotated away from the salt bridge. Consequently, no drastic disruption of the hydrogen-bond network that keeps the loop close to the helices occurs in the variant simulations.
c.767A>G	N256S (3D Viewer)	C2	Likely Pathogenic		1				-10.640	Likely Pathogenic	0.950	Likely Pathogenic	Ambiguous	0.707	Likely Pathogenic	0.31	Likely Benign	0.2	0.36	Likely Benign	0.34	Likely Benign	0.48	Likely Benign	-4.33	Deleterious	0.997	Probably Damaging	0.970	Probably Damaging	5.87	Benign	0.02	Affected	3.39	15	1	1	2.7	-27.03
c.899C>G	S300C (3D Viewer)	C2				6-33437804-C-G			-6.749	Likely Benign	0.108	Likely Benign	Likely Benign	0.129	Likely Benign	0.31	Likely Benign	0.2	1.45	Ambiguous	0.88	Ambiguous	0.34	Likely Benign	-2.45	Neutral	0.975	Probably Damaging	0.815	Possibly Damaging	1.55	Pathogenic	0.01	Affected	3.47	19	-1	0	3.3	16.06
c.670A>G	T224A (3D Viewer)	PH	Uncertain		3	6-33435521-A-G	2	1.24e-6	-7.379	In-Between	0.651	Likely Pathogenic	Likely Benign	0.464	Likely Benign	0.33	Likely Benign	0.1	1.05	Ambiguous	0.69	Ambiguous	0.91	Ambiguous	-2.96	Deleterious	0.243	Benign	0.079	Benign	5.57	Benign	0.57	Tolerated	3.41	13	1	0	2.5	-30.03	169.0	41.4	-0.5	1.1	-0.4	0.0	X	X						Uncertain	The introduced residue Ala224 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Unlike the hydroxyl group of the Thr224 side chain in the WT model, the methyl side chain of Ala224 cannot form hydrogen bonds with nearby residues Ser204, Ser226, and Gly227. Without these hydrogen-bonding interactions at the β sheet surface, the secondary structure element becomes unstable and unfolds during the variant simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1039A>G	T347A (3D Viewer)	C2				6-33437944-A-G	9	5.58e-6	-5.858	Likely Benign	0.086	Likely Benign	Likely Benign	0.093	Likely Benign	0.34	Likely Benign	0.1	0.70	Ambiguous	0.52	Ambiguous	0.70	Ambiguous	-1.52	Neutral	0.031	Benign	0.016	Benign	1.68	Pathogenic	0.42	Tolerated	3.37	25	0	1	2.5	-30.03
c.1609G>A	A537T (3D Viewer)	GAP				6-33438852-G-A	2	1.24e-6	-4.704	Likely Benign	0.097	Likely Benign	Likely Benign	0.210	Likely Benign	0.35	Likely Benign	0.0	0.29	Likely Benign	0.32	Likely Benign	0.37	Likely Benign	-1.41	Neutral	0.953	Possibly Damaging	0.602	Possibly Damaging	-1.27	Pathogenic	0.44	Tolerated	3.37	35	0	1	-2.5	30.03
c.1165T>A	S389T (3D Viewer)	C2				6-33438070-T-A			-5.403	Likely Benign	0.089	Likely Benign	Likely Benign	0.242	Likely Benign	0.36	Likely Benign	0.2	0.11	Likely Benign	0.24	Likely Benign	-0.04	Likely Benign	-0.26	Neutral	0.140	Benign	0.481	Possibly Damaging	5.07	Benign	0.03	Affected	4.32	8	1	1	0.1	14.03
c.1401C>A	D467E (3D Viewer)	GAP				6-33438433-C-A	2	1.24e-6	-9.774	Likely Pathogenic	0.903	Likely Pathogenic	Ambiguous	0.576	Likely Pathogenic	0.36	Likely Benign	0.1	0.87	Ambiguous	0.62	Ambiguous	0.60	Ambiguous	-3.63	Deleterious	0.887	Possibly Damaging	0.938	Probably Damaging	-1.08	Pathogenic	0.04	Affected	3.37	31	2	3	0.0	14.03
c.1412C>G	S471C (3D Viewer)	GAP				6-33438444-C-G	1	6.20e-7	-3.454	Likely Benign	0.093	Likely Benign	Likely Benign	0.273	Likely Benign	0.36	Likely Benign	0.0	-0.05	Likely Benign	0.16	Likely Benign	0.07	Likely Benign	-2.90	Deleterious	0.000	Benign	0.001	Benign	-1.32	Pathogenic	0.01	Affected	3.37	34	-1	0	3.3	16.06
c.901G>A	A301T (3D Viewer)	C2	Uncertain		5	6-33437806-G-A	2	1.24e-6	-3.448	Likely Benign	0.070	Likely Benign	Likely Benign	0.150	Likely Benign	0.36	Likely Benign	0.2	-0.33	Likely Benign	0.02	Likely Benign	0.03	Likely Benign	-0.25	Neutral	0.997	Probably Damaging	0.989	Probably Damaging	4.15	Benign	0.22	Tolerated	4.32	14	1	0	-2.5	30.03	219.8	-42.8	-0.1	0.0	-0.5	0.2								Uncertain	The methyl group of Ala301, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Met289-Pro298, res. Thr305-Asn315), points outward from the β hairpin loop, and its backbone atoms do not participate in the loop formation in the WT simulations. In the variant simulations, the hydroxyl group of the Thr301 side chain also mostly points outward; however, the guanidinium group of Arg299 is moved away from its central hairpin loop position.β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Due to its location near the membrane surface, the residue swap could also affect the C2 loop dynamics and SynGAP-membrane association. However, this is beyond the scope of the solvent-only simulations to unravel.
c.1222A>G	T408A		Uncertain		1				-8.304	Likely Pathogenic	0.114	Likely Benign	Likely Benign	0.118	Likely Benign	0.37	Likely Benign	0.6	-0.06	Likely Benign	0.16	Likely Benign	0.72	Ambiguous	-3.07	Deleterious	0.540	Possibly Damaging	0.131	Benign	4.16	Benign	0.14	Tolerated			1	0	2.5	-30.03
c.1849G>A	E617K (3D Viewer)	GAP				6-33440901-G-A	1	6.20e-7	-10.702	Likely Pathogenic	0.910	Likely Pathogenic	Ambiguous	0.534	Likely Pathogenic	0.37	Likely Benign	0.1	1.19	Ambiguous	0.78	Ambiguous	0.17	Likely Benign	-3.32	Deleterious	0.997	Probably Damaging	0.987	Probably Damaging	-1.34	Pathogenic	0.48	Tolerated	3.37	35	1	0	-0.4	-0.94
c.914C>T	T305I (3D Viewer)	C2				6-33437819-C-T	1	6.20e-7	-5.222	Likely Benign	0.305	Likely Benign	Likely Benign	0.224	Likely Benign	0.37	Likely Benign	0.2	0.58	Ambiguous	0.48	Likely Benign	0.25	Likely Benign	-2.90	Deleterious	0.997	Probably Damaging	0.929	Probably Damaging	1.70	Pathogenic	0.04	Affected	3.40	20	-1	0	5.2	12.05
c.1346G>A	S449N (3D Viewer)	GAP				6-33438251-G-A	1	6.19e-7	-7.692	In-Between	0.209	Likely Benign	Likely Benign	0.070	Likely Benign	0.38	Likely Benign	0.1	-0.03	Likely Benign	0.18	Likely Benign	0.81	Ambiguous	-2.31	Neutral	0.372	Benign	0.026	Benign	3.37	Benign	0.18	Tolerated	3.37	32	1	1	-2.7	27.03
c.1136C>T	S379L (3D Viewer)	C2	Benign		1	6-33438041-C-T	8	4.05e-5	-5.641	Likely Benign	0.173	Likely Benign	Likely Benign	0.469	Likely Benign	0.39	Likely Benign	0.2	3.38	Destabilizing	1.89	Ambiguous	-0.52	Ambiguous	-0.85	Neutral	0.015	Benign	0.002	Benign	3.83	Benign	0.04	Affected	4.32	11	-3	-2	4.6	26.08	251.9	-48.1	0.6	1.1	0.0	0.5								Uncertain	Ser379 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like leucine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Leu379 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1438G>A	E480K (3D Viewer)	GAP				6-33438470-G-A	1	6.20e-7	-14.059	Likely Pathogenic	0.961	Likely Pathogenic	Likely Pathogenic	0.768	Likely Pathogenic	0.40	Likely Benign	0.1	1.08	Ambiguous	0.74	Ambiguous	0.83	Ambiguous	-3.45	Deleterious	0.996	Probably Damaging	0.987	Probably Damaging	-1.26	Pathogenic	0.11	Tolerated	3.37	34	1	0	-0.4	-0.94
c.695C>T	A232V (3D Viewer)	PH				6-33435546-C-T	2	1.24e-6	-9.418	Likely Pathogenic	0.962	Likely Pathogenic	Likely Pathogenic	0.539	Likely Pathogenic	0.40	Likely Benign	0.1	0.23	Likely Benign	0.32	Likely Benign	0.55	Ambiguous	-2.99	Deleterious	0.608	Possibly Damaging	0.240	Benign	5.85	Benign	0.06	Tolerated	3.40	14	0	0	2.4	28.05
c.1040C>A	T347N (3D Viewer)	C2				6-33437945-C-A	9	5.58e-6	-5.545	Likely Benign	0.165	Likely Benign	Likely Benign	0.059	Likely Benign	0.41	Likely Benign	0.1	0.46	Likely Benign	0.44	Likely Benign	-0.06	Likely Benign	1.96	Neutral	0.001	Benign	0.001	Benign	1.67	Pathogenic	0.60	Tolerated	3.37	25	0	0	-2.8	13.00
c.603T>A	D201E (3D Viewer)	PH	Benign		1				-2.640	Likely Benign	0.406	Ambiguous	Likely Benign	0.165	Likely Benign	0.42	Likely Benign	0.2	1.99	Ambiguous	1.21	Ambiguous	0.23	Likely Benign	-0.69	Neutral	0.633	Possibly Damaging	0.108	Benign	4.30	Benign	1.00	Tolerated	3.46	9	3	2	0.0	14.03	258.7	-24.8	0.9	0.1	-0.3	0.2						X		Uncertain	Asp201, an acidic residue located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by another acidic residue, glutamate. The carboxylate groups of both Asp201 and Glu201 side chains form hydrogen bonds with the hydroxyl group of Ser221 in the simulations. Due to its shorter side chain, Asp201 can also hydrogen bond with the backbone amide groups of neighboring loop residues Ser204 and Asp203. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.603T>G	D201E (3D Viewer)	PH	Conflicting		2	6-33435245-T-G	20	1.24e-5	-2.640	Likely Benign	0.406	Ambiguous	Likely Benign	0.165	Likely Benign	0.42	Likely Benign	0.2	1.99	Ambiguous	1.21	Ambiguous	0.23	Likely Benign	-0.69	Neutral	0.633	Possibly Damaging	0.108	Benign	4.30	Benign	1.00	Tolerated	3.46	9	3	2	0.0	14.03	258.7	-24.8	0.9	0.1	-0.3	0.2						X		Uncertain	Asp201, an acidic residue located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by another acidic residue, glutamate. The carboxylate groups of both Asp201 and Glu201 side chains form hydrogen bonds with the hydroxyl group of Ser221 in the simulations. Due to its shorter side chain, Asp201 can also hydrogen bond with the backbone amide groups of neighboring loop residues Ser204 and Asp203. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1438G>C	E480Q (3D Viewer)	GAP				6-33438470-G-C	2	1.24e-6	-12.336	Likely Pathogenic	0.845	Likely Pathogenic	Ambiguous	0.480	Likely Benign	0.43	Likely Benign	0.0	-0.01	Likely Benign	0.21	Likely Benign	0.75	Ambiguous	-2.29	Neutral	0.994	Probably Damaging	0.986	Probably Damaging	-1.29	Pathogenic	0.11	Tolerated	3.37	34	2	2	0.0	-0.98
c.1488G>T	E496D (3D Viewer)	GAP				6-33438520-G-T	2	1.24e-6	-10.552	Likely Pathogenic	0.922	Likely Pathogenic	Ambiguous	0.583	Likely Pathogenic	0.43	Likely Benign	0.2	1.78	Ambiguous	1.11	Ambiguous	1.18	Destabilizing	-2.78	Deleterious	0.996	Probably Damaging	0.989	Probably Damaging	-1.45	Pathogenic	0.04	Affected	3.37	35	2	3	0.0	-14.03
c.1636T>A	C546S (3D Viewer)	GAP				6-33438879-T-A	1	6.20e-7	-8.079	Likely Pathogenic	0.988	Likely Pathogenic	Likely Pathogenic	0.836	Likely Pathogenic	0.44	Likely Benign	0.1	1.39	Ambiguous	0.92	Ambiguous	1.65	Destabilizing	-8.04	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.21	Pathogenic	0.17	Tolerated	3.37	35	-1	0	-3.3	-16.06
c.985C>T	R329C (3D Viewer)	C2				6-33437890-C-T	2	1.24e-6	-9.433	Likely Pathogenic	0.865	Likely Pathogenic	Ambiguous	0.313	Likely Benign	0.44	Likely Benign	0.1	0.40	Likely Benign	0.42	Likely Benign	0.69	Ambiguous	-5.70	Deleterious	0.999	Probably Damaging	0.825	Possibly Damaging	3.98	Benign	0.00	Affected	3.41	15	-3	-4	7.0	-53.05
c.1286G>A	R429Q (3D Viewer)	GAP	Uncertain		2	6-33438191-G-A	10	6.20e-6	-8.227	Likely Pathogenic	0.143	Likely Benign	Likely Benign	0.156	Likely Benign	0.45	Likely Benign	0.1	0.36	Likely Benign	0.41	Likely Benign	0.98	Ambiguous	-1.25	Neutral	1.000	Probably Damaging	0.979	Probably Damaging	3.47	Benign	0.58	Tolerated	3.38	25	1	1	1.0	-28.06	235.8	59.5	0.0	0.0	-0.3	0.4		X						Potentially Pathogenic	The guanidinium group of the Arg429 side chain, located in an α helix (res. Met414-Glu436), either forms a salt bridge with the carboxylate group of an acidic residue (Asp474, Asp467) or an H-bond with the hydroxyl group of Ser471 in an opposing α helix (res. Ala461-Phe476). In the variant simulations, Gln429 cannot form ionic interactions with the acidic residues; however, the carboxamide group can form multiple H-bonds. The H-bonding coordination of the Asn429 side chain varied between the replica simulations. In one simulation, three H-bonds were formed simultaneously with the Asp467 side chain, the backbone carbonyl group of Asn426, and the amide group of Met430 at the end of the same α helix. The residue swap could affect the tertiary structure assembly during folding due to weaker bond formation, but no large-scale negative effects were seen during the simulations.
c.1604G>C	S535T (3D Viewer)	GAP	Benign		1	6-33438847-G-C	14	8.67e-6	-3.886	Likely Benign	0.069	Likely Benign	Likely Benign	0.177	Likely Benign	0.45	Likely Benign	0.1	-0.27	Likely Benign	0.09	Likely Benign	0.17	Likely Benign	-0.81	Neutral	0.000	Benign	0.001	Benign	-1.25	Pathogenic	0.25	Tolerated	3.37	35	1	1	0.1	14.03	201.3	-17.3	-0.1	0.7	-0.2	0.1						X		Potentially Benign	Ser535 is located near the terminal end of an α-helix (res. Ala533-Val560) close to the membrane interface. In the WT simulations, the hydroxyl side chain of Ser535 forms hydrogen bonds with nearby residues (e.g., His539, Glu538) without any specific interactions. These hydrogen bonds disrupt the structure of the terminal end of the α-helix (Ala533-Ser535), causing it to weaken or unfold during the WT simulations. In the variant simulations, Thr535, a hydrophilic residue with a hydroxyl group of almost the same size as Ser, interacts more frequently with the preceding loop residues (e.g., Thr532, Cys531) due to its longer side chain. Regardless, the residue swap is tolerated in the simulations with no negative effects. However, due to its location near the SynGAP-membrane interface, the effect of the residue swap cannot be fully addressed using the SynGAP solvent-only simulations.	10.1016/j.ajhg.2020.11.011
c.743G>A	R248Q (3D Viewer)	PH				6-33435594-G-A	2	1.24e-6	-10.573	Likely Pathogenic	0.979	Likely Pathogenic	Likely Pathogenic	0.739	Likely Pathogenic	0.45	Likely Benign	0.2	1.67	Ambiguous	1.06	Ambiguous	1.05	Destabilizing	-3.34	Deleterious	0.999	Probably Damaging	0.715	Possibly Damaging	5.74	Benign	0.01	Affected	3.41	14	1	1	1.0	-28.06
c.1345A>G	S449G (3D Viewer)	GAP	Uncertain		1	6-33438250-A-G	3	1.86e-6	-5.936	Likely Benign	0.071	Likely Benign	Likely Benign	0.116	Likely Benign	0.47	Likely Benign	0.0	0.55	Ambiguous	0.51	Ambiguous	0.85	Ambiguous	-2.32	Neutral	0.948	Possibly Damaging	0.124	Benign	3.35	Benign	0.13	Tolerated	3.37	32	0	1	0.4	-30.03
c.1635G>A	M545I (3D Viewer)	GAP	Uncertain		1				-8.348	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.592	Likely Pathogenic	0.47	Likely Benign	0.1	0.14	Likely Benign	0.31	Likely Benign	0.63	Ambiguous	-3.61	Deleterious	0.935	Possibly Damaging	0.941	Probably Damaging	-1.27	Pathogenic	0.28	Tolerated	3.37	35	1	2	2.6	-18.03
c.694G>A	A232T (3D Viewer)	PH	Benign		1	6-33435545-G-A	1	6.20e-7	-7.655	In-Between	0.874	Likely Pathogenic	Ambiguous	0.469	Likely Benign	0.47	Likely Benign	0.1	-0.04	Likely Benign	0.22	Likely Benign	0.61	Ambiguous	-1.42	Neutral	0.608	Possibly Damaging	0.240	Benign	5.80	Benign	0.09	Tolerated	3.40	14	1	0	-2.5	30.03	210.8	-42.0	0.5	0.1	0.4	0.5						X		Uncertain	The hydroxyl group of Thr232, located at the end of an anti-parallel β sheet strand (res. Thr228-Ala232), forms hydrogen bonds with nearby residues Glu217, Cys233, and Cys219 in the variant simulations. These hydrogen-bonding interactions at the β sheet surface contribute to the stability of the secondary structure element and prevent it from unfolding. The new hydrogen bond interactions may be more favorable for structural stability than the steric interactions of the methyl side chain of Ala with the side chains of Gln216 and Cys219 in the WT. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1298C>T	A433V (3D Viewer)	GAP				6-33438203-C-T	240	1.49e-4	-8.200	Likely Pathogenic	0.129	Likely Benign	Likely Benign	0.096	Likely Benign	0.48	Likely Benign	0.1	-0.07	Likely Benign	0.21	Likely Benign	0.48	Likely Benign	-2.91	Deleterious	0.994	Probably Damaging	0.527	Possibly Damaging	3.43	Benign	0.04	Affected	3.37	29	0	0	2.4	28.05	214.5	-45.8	0.0	0.0	0.0	0.2						X		Potentially Benign	The methyl group of Ala433, located on the outer surface of an α helix (res. Met414-Glu436), does not interact with any nearby residues in the WT simulations. In the variant simulations, the iso-propyl side chain of Val433, which has a similarly hydrophobic profile as alanine, also does not form any lasting interactions at the helix surface. Accordingly, the residue swap does not negatively affect the protein structure based on the simulations.
c.2111G>A	S704N (3D Viewer)	GAP	Conflicting		3	6-33441370-G-A	27	1.67e-5	-5.917	Likely Benign	0.421	Ambiguous	Likely Benign	0.058	Likely Benign	0.48	Likely Benign	0.1	-0.12	Likely Benign	0.18	Likely Benign	0.54	Ambiguous	-0.49	Neutral	0.771	Possibly Damaging	0.275	Benign	3.39	Benign	0.08	Tolerated	3.47	10	1	1	-2.7	27.03	233.2	-29.1	-0.1	0.0	-0.1	0.1						X		Potentially Benign	Ser704 is located at the end and outer surface of an α-helix (res. Thr704-Gly712), which is connected via a tight turn or loop to another α-helix (res. Asp684-Gln702). The hydroxyl side chain of Ser704 occasionally forms a hydrogen bond with the amide group of Ala707. However, in the variant simulations, the carboxamide side chain of Asn704 achieves more lasting and numerous hydrogen-bonding interactions with the residues at the helix end, such as Glu706, Ala707, and Leu708. Consequently, the residue swap could strengthen the α-helix secondary structure integrity at the helix end, which could have either positive or negative effects on its function.
c.859G>C	D287H (3D Viewer)	C2	Likely Pathogenic		1				-14.518	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.589	Likely Pathogenic	0.48	Likely Benign	0.3	0.32	Likely Benign	0.40	Likely Benign	0.63	Ambiguous	-6.43	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.51	Pathogenic	0.00	Affected	3.38	23	1	-1	0.3	22.05	235.6	3.8	0.1	1.2	0.1	0.1	X	X						Potentially Pathogenic	The carboxylate group of Asp287, located at the beginning of a β hairpin loop connecting two anti-parallel β sheet strands (res. Arg279-Leu286, res. Met289-Pro298), maintains a salt bridge with the guanidinium group of Arg324 in the β sheet during the WT simulations. In the variant simulations, the imidazole ring of the His287 side chain is unable to form a salt bridge with Arg324 or establish any other stable compensatory interactions, which could weaken the beta sandwich assembly of the C2 domain. This destabilization of the C2 domain could adversely affect the stability of the SynGAP-membrane association.
c.962G>A	R321H (3D Viewer)	C2	Uncertain		1	6-33437867-G-A	8	4.96e-6	-8.751	Likely Pathogenic	0.136	Likely Benign	Likely Benign	0.323	Likely Benign	0.48	Likely Benign	0.1	-0.36	Likely Benign	0.06	Likely Benign	0.59	Ambiguous	-1.43	Neutral	1.000	Probably Damaging	0.998	Probably Damaging	1.92	Pathogenic	0.25	Tolerated	3.38	23	2	0	1.3	-19.05	218.5	86.9	1.1	0.0	0.3	0.0						X		Potentially Benign	The guanidinium group of Arg321, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Thr305-Asn315, res. Ala322-Asp330), faces outward without forming any stable interactions in the WT simulations. Similarly, in the variant simulations, the imidazole ring of His321 also points outward without making any stable intra-protein interactions. Thus, the residue swap does not seem to cause adverse effects on the protein structure based on the simulations. However, β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant.
c.1130T>G	M377R (3D Viewer)	C2				6-33438035-T-G			-3.150	Likely Benign	0.219	Likely Benign	Likely Benign	0.471	Likely Benign	0.49	Likely Benign	0.4	4.81	Destabilizing	2.65	Destabilizing	0.69	Ambiguous	-0.64	Neutral	0.004	Benign	0.009	Benign	5.46	Benign	0.18	Tolerated	4.32	12	-1	0	-6.4	24.99
c.2119G>A	A707T (3D Viewer)	GAP				6-33441584-G-A	1	6.20e-7	-0.836	Likely Benign	0.175	Likely Benign	Likely Benign	0.252	Likely Benign	0.50	Ambiguous	0.0	2.36	Destabilizing	1.43	Ambiguous	0.10	Likely Benign	-0.57	Neutral	0.980	Probably Damaging	0.947	Probably Damaging	3.52	Benign	0.44	Tolerated	3.50	9	0	1	-2.5	30.03
c.886T>G	S296A (3D Viewer)	C2	Uncertain		1				-6.847	Likely Benign	0.247	Likely Benign	Likely Benign	0.209	Likely Benign	0.50	Ambiguous	0.3	-0.26	Likely Benign	0.12	Likely Benign	0.35	Likely Benign	-1.79	Neutral	0.992	Probably Damaging	0.987	Probably Damaging	1.97	Pathogenic	0.65	Tolerated	3.40	16	1	1	2.6	-16.00	182.5	26.6	-0.2	0.1	-0.5	0.0		X						Potentially Pathogenic	The hydroxyl group of the Ser296 side chain, located in an anti-parallel β sheet strand (res. Met289-Pro298), stably hydrogen bonds with the carboxylate group of Asp330 in a neighboring β strand (res. Ala322-Asp332). The backbone carbonyl group of Ser296 also hydrogen bonds with the guanidinium group of Arg279 in another nearby β strand (res. Arg279-Cys285). In the variant simulations, the methyl group of the Ala296 side chain cannot hydrogen bond with Asp330, causing the carboxylate group positioning to fluctuate more than in the WT simulations.Although the residue swap does not seem to affect the anti-parallel β sheet assembly during the simulations, it is possible that the Ser296-Asp330 hydrogen bond plays a crucial role in maintaining the C2 domain fold. Notably, because Ser296 is located near the membrane interface, the potential effect of the residue swap on the SynGAP-membrane association cannot be addressed by solvent-only simulations.
c.1111A>C	S371R (3D Viewer)	C2				6-33438016-A-C			-6.415	Likely Benign	0.762	Likely Pathogenic	Likely Benign	0.295	Likely Benign	0.51	Ambiguous	1.2	-0.25	Likely Benign	0.13	Likely Benign	0.57	Ambiguous	-1.17	Neutral	0.396	Benign	0.099	Benign	5.35	Benign	0.26	Tolerated	3.52	18	-1	0	-3.7	69.11
c.1113T>G	S371R (3D Viewer)	C2				6-33438018-T-G	1	1.18e-6	-6.415	Likely Benign	0.762	Likely Pathogenic	Likely Benign	0.340	Likely Benign	0.51	Ambiguous	1.2	-0.25	Likely Benign	0.13	Likely Benign	0.57	Ambiguous	-1.17	Neutral	0.396	Benign	0.099	Benign	5.35	Benign	0.26	Tolerated	3.52	18	-1	0	-3.7	69.11
c.2014A>G	T672A (3D Viewer)	GAP	Benign		1	6-33441273-A-G	3	1.86e-6	-6.524	Likely Benign	0.109	Likely Benign	Likely Benign	0.046	Likely Benign	0.51	Ambiguous	0.3	1.15	Ambiguous	0.83	Ambiguous	0.65	Ambiguous	-3.20	Deleterious	0.006	Benign	0.002	Benign	3.44	Benign	0.12	Tolerated	3.40	25	1	0	2.5	-30.03	188.5	42.5	-0.1	0.3	0.2	0.0		X						Potentially Pathogenic	The hydroxyl group of Thr672, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop itself, such as Lys566, Glu666, and Asn669. In the variant simulations, Ala672 can only form a hydrogen bond with Lys566 via its backbone carbonyl group. Consequently, it cannot maintain the Lys566-Glu666 salt bridge through hydrogen bonding, leading to a significant disruption of the intricate and stable hydrogen-bond network between the loop and the helices.
c.1667A>G	N556S (3D Viewer)	GAP	Uncertain		1	6-33438910-A-G	3	1.86e-6	-6.576	Likely Benign	0.197	Likely Benign	Likely Benign	0.449	Likely Benign	0.52	Ambiguous	0.1	0.14	Likely Benign	0.33	Likely Benign	0.16	Likely Benign	-3.60	Deleterious	1.000	Probably Damaging	0.989	Probably Damaging	-1.22	Pathogenic	0.14	Tolerated	3.37	35	1	1	2.7	-27.03	198.8	31.0	0.0	0.0	-0.5	0.2						X		Potentially Benign	Asn556 is located on the outer surface of an α-helix (res. Ala533-Val560). The carboxamide group of Asn556 forms hydrogen bonds with nearby residues such as Lys553 and Cys552. It also forms a hydrogen bond with the backbone carbonyl group of Cys552, which weakens the α-helix integrity. In the variant simulations, the hydroxyl group of Ser556 forms a more stable hydrogen bond with the backbone carbonyl oxygen of the same helix residue, Cys552, compared to Asn556 in the WT. Serine has a slightly lower propensity to reside in an α-helix than asparagine, which may exacerbate the negative effect on the α-helix integrity. However, the residue swap does not cause negative structural effects during the simulations.
c.2186A>C	N729T (3D Viewer)	GAP				6-33441651-A-C	1	6.20e-7	-1.952	Likely Benign	0.102	Likely Benign	Likely Benign	0.052	Likely Benign	0.52	Ambiguous	0.3	1.73	Ambiguous	1.13	Ambiguous	-0.34	Likely Benign	-0.52	Neutral	0.123	Benign	0.042	Benign	3.33	Benign	1.00	Tolerated	3.59	7	0	0	2.8	-13.00
c.1003C>T	R335C (3D Viewer)	C2	Uncertain		1	6-33437908-C-T	1	6.20e-7	-14.354	Likely Pathogenic	0.938	Likely Pathogenic	Ambiguous	0.277	Likely Benign	0.53	Ambiguous	0.1	0.85	Ambiguous	0.69	Ambiguous	0.46	Likely Benign	-5.69	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.67	Pathogenic	0.01	Affected	3.38	22	-3	-4	7.0	-53.05
c.1154C>G	S385W (3D Viewer)	C2	Benign		1	6-33438059-C-G			-9.353	Likely Pathogenic	0.362	Ambiguous	Likely Benign	0.373	Likely Benign	0.53	Ambiguous	0.2	0.69	Ambiguous	0.61	Ambiguous	0.00	Likely Benign	-0.84	Neutral	0.986	Probably Damaging	0.968	Probably Damaging	4.63	Benign	0.00	Affected	4.32	3	-2	-3	-0.1	99.14	260.4	-71.2	0.5	1.3	0.7	0.4								Uncertain	Ser385 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like tryptophan are rarely tolerated. Although no major negative structural effects are observed in the variant simulations, Trp385 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effects on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.	10.1016/j.ajhg.2020.11.011
c.1925A>C	K642T (3D Viewer)	GAP	Likely Pathogenic		1				-12.823	Likely Pathogenic	0.948	Likely Pathogenic	Ambiguous	0.484	Likely Benign	0.53	Ambiguous	0.1	0.30	Likely Benign	0.42	Likely Benign	0.28	Likely Benign	-5.88	Deleterious	0.872	Possibly Damaging	0.839	Possibly Damaging	2.86	Benign	0.00	Affected	3.37	31	0	-1	3.2	-27.07	213.5	-8.7	-0.3	0.4	0.3	0.2				X				Uncertain	The amino side chain of Lys642, located on the surface of an α helix (res. Ser641-Glu666), is not involved in any interactions in the WT simulations. In the variant simulations, the shorter side chain of Thr642 forms hydrogen bonds with Glu643 and Thr640 on the same α helix.Regardless, Lys642 is positioned directly at the GAP-Ras interface, and in the SynGAP-Ras WT simulations, its amino side chain forms salt bridges with the carboxylate groups of Ras residues Asp33 and Asp38. The shorter Thr642 is more likely to prefer hydrogen bonding with Glu643 and Thr640 on the same α helix, even in the Ras complex. Thus, the effect of the residue swap on the complex formation with the GTPase cannot be explored using solvent-only simulations.
c.2165G>C	S722T (3D Viewer)	GAP				6-33441630-G-C	1	6.20e-7	-5.734	Likely Benign	0.202	Likely Benign	Likely Benign	0.118	Likely Benign	0.53	Ambiguous	0.0	-0.32	Likely Benign	0.11	Likely Benign	-0.12	Likely Benign	-0.57	Neutral	0.921	Possibly Damaging	0.414	Benign	2.57	Benign	1.00	Tolerated	3.50	8	1	1	0.1	14.03
c.1436G>A	R479Q (3D Viewer)	GAP	Uncertain		1	6-33438468-G-A	7	4.34e-6	-7.109	In-Between	0.259	Likely Benign	Likely Benign	0.191	Likely Benign	0.54	Ambiguous	0.1	0.57	Ambiguous	0.56	Ambiguous	0.49	Likely Benign	-1.16	Neutral	1.000	Probably Damaging	0.991	Probably Damaging	3.42	Benign	0.31	Tolerated	3.39	32	1	1	1.0	-28.06
c.1610C>T	A537V (3D Viewer)	GAP	Likely Benign		1	6-33438853-C-T	7	4.34e-6	-6.888	Likely Benign	0.120	Likely Benign	Likely Benign	0.382	Likely Benign	0.54	Ambiguous	0.0	-0.05	Likely Benign	0.25	Likely Benign	0.41	Likely Benign	-1.97	Neutral	0.977	Probably Damaging	0.469	Possibly Damaging	-1.26	Pathogenic	0.24	Tolerated	3.37	35	0	0	2.4	28.05	220.3	-45.1	0.0	0.0	-0.7	0.1						X		Potentially Benign	Ala537 is located on the outer surface of an α-helix (res. Ala533-Val560). The methyl group of Ala537 is on the surface and does not form any interactions. In the variant simulations, the iso-propyl side chain of Val537 is also on the surface, similar to Ala537 in the WT, causing no negative structural effects.
c.2186A>T	N729I (3D Viewer)	GAP				6-33441651-A-T	1	6.20e-7	-3.308	Likely Benign	0.234	Likely Benign	Likely Benign	0.043	Likely Benign	0.54	Ambiguous	0.6	0.79	Ambiguous	0.67	Ambiguous	0.29	Likely Benign	-2.96	Deleterious	0.506	Possibly Damaging	0.243	Benign	3.26	Benign	0.13	Tolerated	3.59	7	-3	-2	8.0	-0.94
c.2006A>G	N669S (3D Viewer)	GAP				6-33441265-A-G	3	1.86e-6	-8.369	Likely Pathogenic	0.187	Likely Benign	Likely Benign	0.210	Likely Benign	0.55	Ambiguous	0.1	1.88	Ambiguous	1.22	Ambiguous	0.35	Likely Benign	-4.02	Deleterious	0.999	Probably Damaging	0.960	Probably Damaging	3.52	Benign	0.14	Tolerated	3.39	27	1	1	2.7	-27.03
c.1211C>T	A404V (3D Viewer)	C2				6-33438116-C-T	1	6.20e-7	-8.219	Likely Pathogenic	0.343	Ambiguous	Likely Benign	0.118	Likely Benign	0.56	Ambiguous	0.3	-1.55	Ambiguous	-0.50	Ambiguous	-0.05	Likely Benign	-2.96	Deleterious	0.345	Benign	0.018	Benign	4.20	Benign	0.47	Tolerated	3.38	28	0	0	2.4	28.05
c.1306G>A	E436K (3D Viewer)	GAP	Uncertain		1				-13.869	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.829	Likely Pathogenic	0.56	Ambiguous	0.1	2.86	Destabilizing	1.71	Ambiguous	0.82	Ambiguous	-3.77	Deleterious	0.994	Probably Damaging	0.951	Probably Damaging	4.71	Benign	0.02	Affected	3.37	29	0	1	-0.4	-0.94	186.8	39.8	0.0	0.0	-0.2	0.0	X	X		X				Potentially Pathogenic	The carboxylate group of Glu436, located on the α helix (res. Met414-Glu436), forms a salt bridge with the amino group of the Lys444 side chain on an opposing α helix (res. Val441-Ser457). The backbone carbonyl of Glu436 also H-bonds with the Lys444 side chain, which helps keep the ends of the two α helices tightly connected. In contrast, in the variant simulations, the salt bridge formation with Lys444 is not possible. Instead, the repelled Lys436 side chain rotates outward, causing a change in the α helix backbone H-bonding: the amide group of Lys444 H-bonds with the carbonyl of Ala433 instead of the carbonyl of Cys432.
c.1478C>T	A493V (3D Viewer)	GAP				6-33438510-C-T	3	1.86e-6	-12.511	Likely Pathogenic	0.952	Likely Pathogenic	Ambiguous	0.735	Likely Pathogenic	0.56	Ambiguous	0.1	-0.67	Ambiguous	-0.06	Likely Benign	0.91	Ambiguous	-3.84	Deleterious	0.999	Probably Damaging	0.988	Probably Damaging	-1.31	Pathogenic	0.10	Tolerated	3.37	35	0	0	2.4	28.05
c.712G>A	E238K (3D Viewer)	PH							-13.475	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.858	Likely Pathogenic	0.56	Ambiguous	0.4	1.83	Ambiguous	1.20	Ambiguous	0.83	Ambiguous	-3.63	Deleterious	0.995	Probably Damaging	0.695	Possibly Damaging	5.46	Benign	0.01	Affected	4.29	391	0	1	-0.4	-0.94	209.0	55.9	0.0	0.0	-0.1	0.0		X						Potentially Pathogenic	The negatively charged residue Glu238, located in an α helix (res. Ala236-Val250), is replaced by the positively charged residue Lys238. This charge reversal removes the periodically formed salt bridge between the carboxylate group of Glu238 and the guanidinium group of Arg234 observed in the WT simulations. In the variant simulations, both Lys238 and Arg234 form alternative salt bridges with the carboxylate group of Glu680 in the GAP domain loop. Although not visible in the simulations, the absence of the Glu238-Arg234 salt bridge could weaken the integrity of the α helix (residues Ala236-Val250) and potentially affect the tertiary assembly between the PH and GAP domains.
c.971G>A	R324Q (3D Viewer)	C2	Uncertain		3	6-33437876-G-A	3	1.86e-6	-5.001	Likely Benign	0.172	Likely Benign	Likely Benign	0.307	Likely Benign	0.56	Ambiguous	0.1	0.63	Ambiguous	0.60	Ambiguous	1.02	Destabilizing	-1.17	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	1.92	Pathogenic	0.41	Tolerated	3.39	22	1	1	1.0	-28.06
c.961C>T	R321C (3D Viewer)	C2	Likely Benign		1	6-33437866-C-T	9	5.58e-6	-10.025	Likely Pathogenic	0.387	Ambiguous	Likely Benign	0.495	Likely Benign	0.57	Ambiguous	0.1	0.56	Ambiguous	0.57	Ambiguous	0.18	Likely Benign	-4.59	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.89	Pathogenic	0.01	Affected	3.38	23	-3	-4	7.0	-53.05
c.1004G>A	R335H (3D Viewer)	C2	Uncertain		1	6-33437909-G-A	2	1.24e-6	-12.521	Likely Pathogenic	0.831	Likely Pathogenic	Ambiguous	0.132	Likely Benign	0.58	Ambiguous	0.1	0.22	Likely Benign	0.40	Likely Benign	0.72	Ambiguous	-3.02	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.70	Pathogenic	0.03	Affected	3.38	22	2	0	1.3	-19.05	242.4	82.1	-2.4	0.6	-0.1	0.1								Uncertain	The guanidinium group of Arg335, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Ala322-Asp330, res. Gly341-Pro349), faces the post-synaptic inner membrane surface. In the WT simulations, the Arg335 side chain dynamically forms salt bridges with the carboxylate groups of Asp322, Asp338, and Asp616. In contrast, the imidazole ring of His335, which is not double protonated and thus not positively charged in the variant simulations, continues to move dynamically without forming any lasting or strong interactions. Importantly, the positively charged arginine residues of the C2 domain are ideal membrane anchors for ensuring SynGAP-membrane association. However, this phenomenon cannot be addressed using solvent-only simulations.
c.1067G>A	R356H (3D Viewer)	C2	Likely Benign		1	6-33437972-G-A	9	5.66e-6	-11.453	Likely Pathogenic	0.614	Likely Pathogenic	Likely Benign	0.314	Likely Benign	0.59	Ambiguous	0.1	-0.27	Likely Benign	0.16	Likely Benign	1.17	Destabilizing	-4.43	Deleterious	0.999	Probably Damaging	0.987	Probably Damaging	1.70	Pathogenic	0.01	Affected	3.39	22	0	2	1.3	-19.05
c.1221G>T	Q407H (3D Viewer)	C2	Uncertain		1				-10.526	Likely Pathogenic	0.830	Likely Pathogenic	Ambiguous	0.206	Likely Benign	0.59	Ambiguous	0.0	0.61	Ambiguous	0.60	Ambiguous	1.10	Destabilizing	-4.51	Deleterious	0.982	Probably Damaging	0.947	Probably Damaging	3.88	Benign	0.01	Affected	3.38	28	0	3	0.3	9.01
c.1435C>T	R479W (3D Viewer)	GAP				6-33438467-C-T	6	3.72e-6	-11.356	Likely Pathogenic	0.783	Likely Pathogenic	Likely Benign	0.249	Likely Benign	0.60	Ambiguous	0.1	0.72	Ambiguous	0.66	Ambiguous	0.42	Likely Benign	-4.75	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	3.35	Benign	0.02	Affected	3.39	32	-3	2	3.6	30.03
c.758A>G	N253S (3D Viewer)	PH				6-33435609-A-G			-7.197	In-Between	0.541	Ambiguous	Likely Benign	0.716	Likely Pathogenic	0.60	Ambiguous	0.1	1.19	Ambiguous	0.90	Ambiguous	-0.03	Likely Benign	-4.26	Deleterious	0.993	Probably Damaging	0.956	Probably Damaging	5.56	Benign	0.09	Tolerated	3.39	15	1	1	2.7	-27.03
c.707C>T	A236V (3D Viewer)	PH	Benign/Likely benign		2	6-33435558-C-T	6	3.72e-6	-8.752	Likely Pathogenic	0.267	Likely Benign	Likely Benign	0.777	Likely Pathogenic	0.61	Ambiguous	0.2	1.08	Ambiguous	0.85	Ambiguous	0.64	Ambiguous	-3.55	Deleterious	0.981	Probably Damaging	0.446	Benign	5.79	Benign	0.03	Affected	3.40	14	0	0	2.4	28.05	213.8	-44.7	0.0	0.0	-0.2	0.2						X		Potentially Benign	The methyl side chain of Ala236, located on an α helix (residues Ala236-Val250) facing an anti-parallel β sheet strand (residues Ile205-Val209), interacts hydrophobically with nearby residues such as Arg239 and Phe218. In the variant simulations, the isopropyl branched hydrocarbon side chain of Val236 maintains similar hydrophobic interactions as alanine in the WT, with an overall arrangement remarkably similar to Ala236. The residue swap does not affect the protein structure based on the simulations.
c.1659G>C	K553N (3D Viewer)	GAP				6-33438902-G-C	1	6.20e-7	-13.664	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.566	Likely Pathogenic	0.63	Ambiguous	0.0	0.62	Ambiguous	0.63	Ambiguous	1.11	Destabilizing	-4.77	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.24	Pathogenic	0.11	Tolerated	3.37	35	0	1	0.4	-14.07
c.1667A>T	N556I (3D Viewer)	GAP	Likely Benign		1	6-33438910-A-T			-13.391	Likely Pathogenic	0.929	Likely Pathogenic	Ambiguous	0.761	Likely Pathogenic	0.64	Ambiguous	0.0	0.17	Likely Benign	0.41	Likely Benign	0.26	Likely Benign	-7.52	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.35	Pathogenic	0.02	Affected	3.37	35	-3	-2	8.0	-0.94
c.1061C>T	A354V (3D Viewer)	C2				6-33437966-C-T	1	6.26e-7	-6.223	Likely Benign	0.122	Likely Benign	Likely Benign	0.027	Likely Benign	0.65	Ambiguous	0.1	-1.02	Ambiguous	-0.19	Likely Benign	0.18	Likely Benign	-1.11	Neutral	0.146	Benign	0.038	Benign	1.81	Pathogenic	0.05	Affected	3.38	24	0	0	2.4	28.05
c.1736G>A	R579Q (3D Viewer)	GAP				6-33440788-G-A	18	1.12e-5	-9.193	Likely Pathogenic	0.690	Likely Pathogenic	Likely Benign	0.673	Likely Pathogenic	0.65	Ambiguous	0.1	0.70	Ambiguous	0.68	Ambiguous	1.13	Destabilizing	-3.31	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	-1.34	Pathogenic	0.06	Tolerated	3.37	34	1	1	1.0	-28.06
c.611C>G	S204C (3D Viewer)	PH	Uncertain		1				-6.613	Likely Benign	0.127	Likely Benign	Likely Benign	0.148	Likely Benign	0.65	Ambiguous	0.4	-1.13	Ambiguous	-0.24	Likely Benign	0.10	Likely Benign	-0.64	Neutral	0.978	Probably Damaging	0.753	Possibly Damaging	4.13	Benign	0.05	Affected	3.44	10	0	-1	3.3	16.06	223.6	-13.8	0.6	0.3	0.0	0.2	X							Uncertain	The hydroxyl-containing Ser204, located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by the thiol-containing cysteine. In the WT simulations, Ser204 simultaneously forms hydrogen bonds with the backbone carbonyl of Asp201 and the hydroxyl group of Thr224, helping to stabilize the two anti-parallel β strands (res. Ile205-Lys207 and Cys219-Thr223) at the end of the β sheet. Since the thiol group of cysteine forms weaker hydrogen bonds than the hydroxyl group of serine, Cys204 does not maintain the hydrogen bond network as stably as Ser204 in the variant simulations. However, because the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1120T>C	S374P (3D Viewer)	C2				6-33438025-T-C	1	7.85e-7	-4.849	Likely Benign	0.125	Likely Benign	Likely Benign	0.388	Likely Benign	0.66	Ambiguous	0.6	2.22	Destabilizing	1.44	Ambiguous	0.34	Likely Benign	-0.89	Neutral	0.396	Benign	0.099	Benign	5.30	Benign	0.02	Affected	4.32	13	-1	1	-0.8	10.04
c.1463C>T	T488M (3D Viewer)	GAP	Uncertain		1	6-33438495-C-T	2	1.24e-6	-12.459	Likely Pathogenic	0.973	Likely Pathogenic	Likely Pathogenic	0.746	Likely Pathogenic	0.66	Ambiguous	0.3	1.62	Ambiguous	1.14	Ambiguous	0.46	Likely Benign	-5.70	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	3.21	Benign	0.00	Affected	3.37	35	-1	-1	2.6	30.09
c.1622C>G	A541G (3D Viewer)	GAP	Uncertain		1	6-33438865-C-G	2	1.24e-6	-7.233	In-Between	0.341	Ambiguous	Likely Benign	0.421	Likely Benign	0.67	Ambiguous	0.0	0.94	Ambiguous	0.81	Ambiguous	0.76	Ambiguous	-1.48	Neutral	0.999	Probably Damaging	0.995	Probably Damaging	-1.31	Pathogenic	0.57	Tolerated	3.37	35	1	0	-2.2	-14.03	170.1	23.6	0.0	0.0	0.0	0.0	X							Potentially Pathogenic	Ala541 is located on the outer surface of an α-helix (res. Ala533-Val560). The methyl group of Ala541 is on the surface and does not form any interactions. Glycine, known as an “α-helix breaker,” weakens the integrity of the helix. Indeed, in the variant simulations, the hydrogen bond formation between Gly541 and the backbone carbonyl of Ala537 is disrupted.
c.1750A>G	I584V (3D Viewer)	GAP				6-33440802-A-G	1	6.20e-7	-7.562	In-Between	0.234	Likely Benign	Likely Benign	0.405	Likely Benign	0.67	Ambiguous	0.1	0.29	Likely Benign	0.48	Likely Benign	1.16	Destabilizing	-0.95	Neutral	0.642	Possibly Damaging	0.349	Benign	-1.18	Pathogenic	0.18	Tolerated	3.37	34	3	4	-0.3	-14.03
c.1768A>G	S590G (3D Viewer)	GAP	Likely Benign		1	6-33440820-A-G	14	8.67e-6	-14.277	Likely Pathogenic	0.574	Likely Pathogenic	Likely Benign	0.379	Likely Benign	0.67	Ambiguous	0.1	1.28	Ambiguous	0.98	Ambiguous	0.71	Ambiguous	-3.92	Deleterious	1.000	Probably Damaging	0.922	Probably Damaging	3.42	Benign	0.06	Tolerated	3.37	35	1	0	0.4	-30.03	186.7	49.4	0.0	0.0	0.1	0.0		X						Potentially Pathogenic	In the WT simulations, the hydroxyl group of Ser590, located on an α helix (res. Glu582-Met603), forms hydrogen bonds with the backbone carbonyl of Ala634 and/or the carboxamide group of the Asn635 side chain at the end of the opposing α helix (res. Thr619-Ala634).The residue swap could weaken the integrity of the α helix, as glycine is known as an “α helix breaker.” However, no discernible difference was observed between the WT and variant simulations in this regard. Importantly, Gly590 cannot form hydrogen bonds with the opposing helix in the same way that serine can, which could weaken the tertiary structure assembly between the two helices.
c.1940G>A	G647D (3D Viewer)	GAP				6-33441199-G-A	1	6.20e-7	-7.643	In-Between	0.582	Likely Pathogenic	Likely Benign	0.098	Likely Benign	0.68	Ambiguous	0.1	0.33	Likely Benign	0.51	Ambiguous	0.56	Ambiguous	-1.63	Neutral	0.282	Benign	0.128	Benign	3.45	Benign	0.24	Tolerated	3.37	30	-1	1	-3.1	58.04
c.1386G>T	K462N (3D Viewer)	GAP				6-33438291-G-T	1	6.20e-7	-12.823	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.303	Likely Benign	0.69	Ambiguous	0.1	1.67	Ambiguous	1.18	Ambiguous	0.90	Ambiguous	-4.83	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	3.42	Benign	0.07	Tolerated	3.37	34	0	1	0.4	-14.07
c.1730C>T	A577V (3D Viewer)	GAP				6-33440782-C-T	2	1.24e-6	-4.265	Likely Benign	0.432	Ambiguous	Likely Benign	0.417	Likely Benign	0.69	Ambiguous	0.1	0.00	Likely Benign	0.35	Likely Benign	0.16	Likely Benign	-2.11	Neutral	0.997	Probably Damaging	0.976	Probably Damaging	-1.32	Pathogenic	0.26	Tolerated	3.37	34	0	0	2.4	28.05
c.1121C>A	S374Y (3D Viewer)	C2	Uncertain		1				-7.774	In-Between	0.344	Ambiguous	Likely Benign	0.310	Likely Benign	0.71	Ambiguous	1.2	0.66	Ambiguous	0.69	Ambiguous	-0.02	Likely Benign	-1.18	Neutral	0.875	Possibly Damaging	0.271	Benign	5.41	Benign	0.01	Affected	4.32	13	-3	-2	-0.5	76.10	237.3	-76.9	0.5	0.4	0.5	0.3								Uncertain	Ser374 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus, large and relatively hydrophobic residues like tyrosine are rarely tolerated. Additionally, the hydroxyl group of Tyr374 frequently forms various hydrogen bonds with other loop residues in the variant simulations. Although no negative structural effects are observed in the variant simulations, Tyr374 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1424G>A	R475Q (3D Viewer)	GAP	Uncertain		2	6-33438456-G-A	5	3.10e-6	-12.087	Likely Pathogenic	0.721	Likely Pathogenic	Likely Benign	0.632	Likely Pathogenic	0.71	Ambiguous	0.1	0.12	Likely Benign	0.42	Likely Benign	0.82	Ambiguous	-3.65	Deleterious	1.000	Probably Damaging	0.991	Probably Damaging	-1.32	Pathogenic	0.01	Affected	3.39	28	1	1	1.0	-28.06	253.6	52.7	0.0	0.0	-0.8	0.0	X	X		X				Potentially Pathogenic	In the WT simulations, the guanidinium group of Arg475, located near the end of an α-helix (res. Ala461-Phe476), stacks with the phenyl ring of Phe476 and forms a salt bridge with Glu472. Additionally, Arg475 occasionally forms another salt bridge with the carboxylate group of Glu486 on the α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. Therefore, Arg475 potentially plays a key role in positioning the loop by interacting with Glu486, which is necessary for the positioning of the “arginine finger” (Arg485) and, ultimately, for RasGTPase activation. In the variant simulations, Asn475 forms a hydrogen bond with Arg479 on the proceeding α-α loop. The absence of Phe476/Arg475 stacking and the Arg475-Glu472 salt bridge weakens the integrity of the terminal end of the α-helix during the variant simulations. Lastly, the potential effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1064G>A	G355E (3D Viewer)	C2				6-33437969-G-A	2	1.24e-6	-9.395	Likely Pathogenic	0.891	Likely Pathogenic	Ambiguous	0.349	Likely Benign	0.72	Ambiguous	0.6	0.63	Ambiguous	0.68	Ambiguous	0.54	Ambiguous	-6.69	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.80	Pathogenic	0.04	Affected	3.38	24	-2	0	-3.1	72.06
c.1213C>T	R405C (3D Viewer)	C2	Conflicting		2	6-33438118-C-T	6	3.72e-6	-9.206	Likely Pathogenic	0.706	Likely Pathogenic	Likely Benign	0.427	Likely Benign	0.72	Ambiguous	0.1	1.51	Ambiguous	1.12	Ambiguous	1.21	Destabilizing	-7.27	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.61	Benign	0.02	Affected	3.38	28	-4	-3	7.0	-53.05	221.3	82.6	-0.1	0.0	-0.2	0.3	X	X						Potentially Pathogenic	The guanidinium group of Arg405, located in an anti-parallel β sheet strand of the C2 domain (res. Ala399-Ile411), forms a salt bridge with the carboxylate group of the Glu446 side chain from an opposing α helix (res. Val441-Ser457) in the GAP domain. The positively charged Arg405 side chain also stacks with the aromatic ring of the Phe358 side chain from a loop preceding the β strand (res. Thr359-Thr366), which could assist in maintaining the anti-parallel strand arrangement.In the variant simulations, the thiol-containing side chain of Cys405 is neutral and smaller compared to the arginine side chain. The lack of Arg405-Phe358 stacking affects the loop structure, causing it to assume a β strand form—an effect that could be exacerbated during protein folding. Moreover, the inability of Cys405 to form a salt bridge with Glu446 could affect the tertiary structure assembly, although this is not apparent based on the variant simulations.
c.1408A>C	M470L (3D Viewer)	GAP	Likely Benign		1	6-33438440-A-C	1	6.20e-7	-8.993	Likely Pathogenic	0.406	Ambiguous	Likely Benign	0.678	Likely Pathogenic	0.73	Ambiguous	0.1	0.84	Ambiguous	0.79	Ambiguous	1.04	Destabilizing	-2.72	Deleterious	0.484	Possibly Damaging	0.654	Possibly Damaging	-1.22	Pathogenic	0.16	Tolerated	3.37	34	4	2	1.9	-18.03	225.3	17.9	0.0	0.0	-0.8	0.5						X		Potentially Benign	The thioether group of Met470, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues in the inter-helix space (e.g., Val473, Leu558) formed by two other α helices (res. Ser604–Arg581, res. Pro562–Arg579). In the WT simulations, Met470 also packs against the positively charged guanidinium groups of Arg575, Arg429, and Arg579, which form salt bridges with the negatively charged carboxylate groups of the Asp474 and Asp467 side chains at the protein surface. In the variant simulations, the iso-butyl side chain of Leu470 packs similarly with the hydrophobic residues as methionine, resulting in no negative effects on the protein structure during the simulation.
c.762G>C	K254N (3D Viewer)	PH	Uncertain		1				-13.306	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.757	Likely Pathogenic	0.73	Ambiguous	0.2	1.87	Ambiguous	1.30	Ambiguous	1.19	Destabilizing	-4.23	Deleterious	0.384	Benign	0.070	Benign	5.93	Benign	0.01	Affected	3.39	15	1	0	0.4	-14.07	215.3	-21.0	-1.0	1.7	0.2	0.3		X						Potentially Pathogenic	The amino group of Lys254, located in an α-β loop connecting the PH and C2 domains (res. Lys251-Arg258), forms salt bridges with the carboxylate groups of Glu244 and Asp684. Since the neutral carboxamide group of the Asn254 side chain cannot form salt bridges with acidic residues, the residue swap potentially weakens the tertiary structure assembly and/or influences the loop positioning. Regardless, in both the variant and WT simulations, all hydrogen bonds formed by the residue’s side chain were broken, and the residue rotated outwards. The partially α helical conformation of the loop, which extends to a nearby α helix (res. Met414-Asn426), is dynamic, making it unclear if the mutation affects it.
c.815G>A	R272Q (3D Viewer)	C2	Uncertain		2	6-33437720-G-A	14	8.67e-6	-9.559	Likely Pathogenic	0.286	Likely Benign	Likely Benign	0.321	Likely Benign	0.73	Ambiguous	0.1	0.15	Likely Benign	0.44	Likely Benign	1.00	Destabilizing	-1.81	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	1.88	Pathogenic	0.03	Affected	3.38	19	1	1	1.0	-28.06	255.7	52.9	0.0	0.0	-0.2	0.1				X				Uncertain	The guanidinium group of Arg272, located at the end of an anti-parallel β sheet strand (res. Arg259-Arg272), is stably maintained in an upright and outward position via stacking with the indole ring of the Trp362 side chain in another β strand (res. Thr359-Pro364). In the WT simulations, Arg272 forms hydrogen bonds with the glycine-rich Ω loop residues (res. Val365-Pro398, e.g., Gly380) and creates a salt bridge with the carboxylate group of the Asp304 side chain.In the variant simulations, the carboxamide group of the Gln272 side chain does not stack with the indole ring of Trp362 as stably as the guanidinium group of Arg272 in the WT. Consequently, the Gln272 side chain is freer to interact with the loop residues than Arg272, potentially negatively affecting the dynamic SynGAP-membrane association. Additionally, Arg272 faces the RasGTPase interface, so the residue swap could impact the SynGAP-Ras complex formation and GTPase activation.
c.866T>C	M289T	C2	Uncertain		1				-4.668	Likely Benign	0.238	Likely Benign	Likely Benign	0.222	Likely Benign	0.73	Ambiguous	0.1	0.17	Likely Benign	0.45	Likely Benign	-0.01	Likely Benign	-0.47	Neutral	0.801	Possibly Damaging	0.315	Benign	1.83	Pathogenic	0.57	Tolerated			-1	-1	-2.6	-30.09
c.1231A>G	I411V (3D Viewer)	GAP	Likely Benign		1				-6.290	Likely Benign	0.385	Ambiguous	Likely Benign	0.212	Likely Benign	0.74	Ambiguous	0.0	0.82	Ambiguous	0.78	Ambiguous	0.99	Ambiguous	-0.86	Neutral	0.935	Possibly Damaging	0.858	Possibly Damaging	3.90	Benign	0.27	Tolerated	3.38	28	4	3	-0.3	-14.03	233.3	28.2	-0.2	0.0	-0.2	0.0						X		Potentially Benign	The sec-butyl side chain of Ile411, located in the hydrophobic space between an anti-parallel β sheet strand (res. Pro398-Ile411) and an α helix (res. Asp684-Gln702), packs against multiple residues (e.g., Met409, Arg259). In the variant simulations, the side chain of Val411 is able to favorably fill the same hydrophobic niche despite its slightly smaller size. In short, the residue swap has no apparent negative effect on the structure based on the simulations.
c.1767C>G	I589M (3D Viewer)	GAP	Uncertain		1				-12.225	Likely Pathogenic	0.926	Likely Pathogenic	Ambiguous	0.830	Likely Pathogenic	0.74	Ambiguous	0.2	1.54	Ambiguous	1.14	Ambiguous	1.33	Destabilizing	-2.99	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.94	Pathogenic	0.00	Affected	3.37	35	2	1	-2.6	18.03	267.6	-24.5	0.0	0.0	-0.1	0.1						X		Potentially Benign	A hydrophobic residue, Ile589, located in an α helix (res. Glu582-Met603), is swapped for another hydrophobic residue, methionine. The sec-butyl hydrocarbon side chain of Ile589 packs favourably with multiple residues in the inter-helix hydrophobic space (e.g., Phe569, Ile667, and Leu664).Although the S-methyl thioether group of the Met589 side chain in the variant is longer than the branched side chain of isoleucine, it stacks favourably with the aromatic phenol ring. Additionally, the polar sulphur atom forms a weak hydrogen bond with the guanidinium group of Arg573, which in turn forms a salt bridge with the carboxylate group of Asp586.Overall, the hydrophobic packing in the inter-helix space does not appear to be disrupted in the variant simulations.
c.1943T>A	F648Y (3D Viewer)	GAP				6-33441202-T-A	4	2.48e-6	-8.632	Likely Pathogenic	0.889	Likely Pathogenic	Ambiguous	0.407	Likely Benign	0.74	Ambiguous	0.1	0.94	Ambiguous	0.84	Ambiguous	1.11	Destabilizing	-2.99	Deleterious	0.984	Probably Damaging	0.913	Probably Damaging	3.41	Benign	0.11	Tolerated	3.37	30	3	7	-4.1	16.00
c.2115G>C	K705N (3D Viewer)	GAP	Likely Pathogenic		1				-9.767	Likely Pathogenic	0.925	Likely Pathogenic	Ambiguous	0.183	Likely Benign	0.74	Ambiguous	0.0	0.37	Likely Benign	0.56	Ambiguous	0.44	Likely Benign	-3.12	Deleterious	0.996	Probably Damaging	0.876	Possibly Damaging	3.37	Benign	0.02	Affected	3.47	10	1	0	0.4	-14.07	221.4	-20.2	0.0	0.0	0.0	0.1						X		Uncertain	The amino side chain of Lys705, located at the end and outer surface of an α-helix (res. Thr704-Gly712), does not form any interactions in the WT simulations. In the variant simulations, the carboxamide side chain of Asn705 briefly forms a salt bridge with Glu706. However, there is no apparent difference between the systems. Due to the model ending abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.1261G>A	A421T (3D Viewer)	GAP				6-33438166-G-A	1	6.19e-7	-9.217	Likely Pathogenic	0.975	Likely Pathogenic	Likely Pathogenic	0.179	Likely Benign	0.75	Ambiguous	0.2	0.18	Likely Benign	0.47	Likely Benign	0.99	Ambiguous	-3.12	Deleterious	0.353	Benign	0.136	Benign	3.43	Benign	0.09	Tolerated	3.37	29	0	1	-2.5	30.03
c.1066C>T	R356C (3D Viewer)	C2	Likely Benign		1	6-33437971-C-T	5	3.10e-6	-11.827	Likely Pathogenic	0.774	Likely Pathogenic	Likely Benign	0.312	Likely Benign	0.76	Ambiguous	0.0	1.19	Ambiguous	0.98	Ambiguous	0.84	Ambiguous	-7.12	Deleterious	1.000	Probably Damaging	0.990	Probably Damaging	1.67	Pathogenic	0.00	Affected	3.39	22	-4	-3	7.0	-53.05	212.3	91.0	-0.1	0.3	-0.3	0.1		X						Potentially Pathogenic	Arg356 is located in a loop that includes a short helical section and connects two anti-parallel β sheet strands (res. Gly341-Pro349, res. Thr359-Pro364). In the WT simulations, the guanidinium group of Arg356 alternately forms salt bridges with the carboxylate groups of the GAP domain residues, Glu446 and Glu698. Arg356 also forms hydrogen bonds with the hydroxyl group of the GAP domain residue Thr691 and interacts with Met409 at the C2-GAP interface.In the variant simulations, the Cys356 mutation fails to maintain any of the Arg356 interactions and only occasionally forms weak hydrogen bonds with nearby C2 domain residues (e.g., Gln407). Although no negative structural effects are observed during the simulations, Arg356 is located at the C2 and GAP domain interface, making the residue swap potentially detrimental to the tertiary structure assembly.
c.1131G>A	M377I (3D Viewer)	C2				6-33438036-G-A	1	6.23e-7	-2.895	Likely Benign	0.212	Likely Benign	Likely Benign	0.227	Likely Benign	0.76	Ambiguous	0.3	0.54	Ambiguous	0.65	Ambiguous	0.24	Likely Benign	-0.41	Neutral	0.000	Benign	0.001	Benign	5.46	Benign	0.26	Tolerated	4.32	12	1	2	2.6	-18.03
c.1690G>A	E564K (3D Viewer)	GAP				6-33440742-G-A			-15.834	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.854	Likely Pathogenic	0.76	Ambiguous	0.1	2.06	Destabilizing	1.41	Ambiguous	0.89	Ambiguous	-3.95	Deleterious	0.997	Probably Damaging	0.987	Probably Damaging	-1.35	Pathogenic	0.10	Tolerated	3.37	35	1	0	-0.4	-0.94
c.1454G>A	R485H (3D Viewer)	GAP				6-33438486-G-A	13	8.05e-6	-13.628	Likely Pathogenic	0.948	Likely Pathogenic	Ambiguous	0.618	Likely Pathogenic	0.77	Ambiguous	0.1	0.12	Likely Benign	0.45	Likely Benign	1.13	Destabilizing	-4.97	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.93	Pathogenic	0.00	Affected	3.37	35	0	2	1.3	-19.05
c.1649C>T	A550V (3D Viewer)	GAP				6-33438892-C-T	1	6.20e-7	-10.461	Likely Pathogenic	0.441	Ambiguous	Likely Benign	0.540	Likely Pathogenic	0.77	Ambiguous	0.2	-0.05	Likely Benign	0.36	Likely Benign	0.48	Likely Benign	-2.93	Deleterious	0.984	Probably Damaging	0.494	Possibly Damaging	-1.05	Pathogenic	0.39	Tolerated	3.37	33	0	0	2.4	28.05
c.1884G>T	K628N (3D Viewer)	GAP				6-33440936-G-T	1	6.20e-7	-12.284	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.403	Likely Benign	0.78	Ambiguous	0.1	0.59	Ambiguous	0.69	Ambiguous	1.11	Destabilizing	-4.98	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.37	Pathogenic	0.00	Affected	3.37	34	0	1	0.4	-14.07
c.1784T>A	L595Q (3D Viewer)	GAP	Uncertain		1				-15.101	Likely Pathogenic	0.984	Likely Pathogenic	Likely Pathogenic	0.733	Likely Pathogenic	0.79	Ambiguous	0.1	1.40	Ambiguous	1.10	Ambiguous	1.99	Destabilizing	-5.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.75	Benign	0.00	Affected	3.37	35	-2	-2	-7.3	14.97
c.1336G>A	E446K (3D Viewer)	GAP				6-33438241-G-A	1	6.19e-7	-14.140	Likely Pathogenic	0.953	Likely Pathogenic	Ambiguous	0.518	Likely Pathogenic	0.80	Ambiguous	0.4	1.57	Ambiguous	1.19	Ambiguous	0.81	Ambiguous	-3.75	Deleterious	0.994	Probably Damaging	0.975	Probably Damaging	3.36	Benign	0.01	Affected	3.38	31	1	0	-0.4	-0.94
c.1468G>A	A490T (3D Viewer)	GAP				6-33438500-G-A	1	6.20e-7	-10.266	Likely Pathogenic	0.891	Likely Pathogenic	Ambiguous	0.821	Likely Pathogenic	0.80	Ambiguous	0.2	1.70	Ambiguous	1.25	Ambiguous	1.00	Destabilizing	-3.87	Deleterious	0.998	Probably Damaging	0.993	Probably Damaging	-1.34	Pathogenic	0.03	Affected	3.37	35	0	1	-2.5	30.03
c.1570T>A	C524S (3D Viewer)	GAP				6-33438813-T-A	1	6.20e-7	-11.174	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.915	Likely Pathogenic	0.80	Ambiguous	0.1	1.55	Ambiguous	1.18	Ambiguous	1.58	Destabilizing	-9.94	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.38	Pathogenic	0.00	Affected	3.37	35	-1	0	-3.3	-16.06
c.1904A>G	N635S (3D Viewer)	GAP	Conflicting		4	6-33440956-A-G	10	6.20e-6	-9.002	Likely Pathogenic	0.101	Likely Benign	Likely Benign	0.104	Likely Benign	0.80	Ambiguous	0.1	0.67	Ambiguous	0.74	Ambiguous	0.95	Ambiguous	-4.45	Deleterious	0.261	Benign	0.044	Benign	3.06	Benign	0.05	Affected	3.37	34	1	1	2.7	-27.03	196.0	30.9	0.1	0.0	-0.3	0.2				X				Uncertain	In the WT simulations, the carboxamide side chain of Asn635, located on the outer surface of an α helix (res. Glu617-Asn635), forms hydrogen bonds with Gln631 on the same α helix and with the hydroxyl side chain of Ser590 on an opposing α helix (res. Glu582-Met603).In the variant simulations, the side chain of Ser635 is shorter than asparagine and thus prefers to hydrogen bond with the carbonyl group of Gln631 on the same helix and, to a lesser extent, with Ser590 compared to Asn635 in the WT. Ser635 forms hydrogen bonds with the backbone atoms of the same helix, which may destabilize the helix, although this is not clearly evident in the simulations. The weakening of the hydrogen bond between Ser635 and Ser590 in the variant may also weaken the tertiary structure assembly between the helices.Additionally, Asn635 is at the GTPase interface. However, the implication of the residue swap on the complex formation with the GTPase cannot be investigated using solvent-only simulations.
c.2111G>C	S704T (3D Viewer)	GAP	Uncertain		1				-4.930	Likely Benign	0.265	Likely Benign	Likely Benign	0.071	Likely Benign	0.80	Ambiguous	0.0	0.15	Likely Benign	0.48	Likely Benign	0.29	Likely Benign	-1.72	Neutral	0.525	Possibly Damaging	0.107	Benign	3.45	Benign	0.07	Tolerated	3.47	10	1	1	0.1	14.03	201.7	-18.0	0.0	0.0	-0.2	0.7						X		Potentially Benign	Ser704 is located at the end and outer surface of an α-helix (res. Thr704-Gly712), which is connected via a tight turn or loop to another α-helix (res. Asp684-Gln702). The hydroxyl side chain of Ser704 occasionally forms a hydrogen bond with the amide group of Ala707. Similarly, in the variant simulations, the hydroxyl side chain of Thr704 forms hydrogen bonds with the amide groups of Ala707 and Leu708. Thus, the residue swap does not cause any apparent structural change.
c.1335G>C	E445D (3D Viewer)	GAP				6-33438240-G-C	4	2.48e-6	-10.238	Likely Pathogenic	0.783	Likely Pathogenic	Likely Benign	0.136	Likely Benign	0.81	Ambiguous	0.0	0.49	Likely Benign	0.65	Ambiguous	0.91	Ambiguous	-2.86	Deleterious	0.977	Probably Damaging	0.921	Probably Damaging	3.54	Benign	0.09	Tolerated	3.38	31	2	3	0.0	-14.03
c.1724G>A	R575H (3D Viewer)	GAP	Conflicting		4	6-33440776-G-A	204	1.27e-4	-11.142	Likely Pathogenic	0.496	Ambiguous	Likely Benign	0.707	Likely Pathogenic	0.81	Ambiguous	0.2	-0.22	Likely Benign	0.30	Likely Benign	1.31	Destabilizing	-2.34	Neutral	1.000	Probably Damaging	0.998	Probably Damaging	-1.33	Pathogenic	0.05	Affected	3.37	35	2	0	1.3	-19.05	244.7	80.6	0.0	0.0	0.3	0.0		X						Potentially Pathogenic	The guanidinium group of Arg575, located in an α-helix (res. Arg563-Glu578), forms salt bridges with the carboxylate groups of Asp463 and Asp467, and it also hydrogen bonds with the hydroxyl group of Ser466 on an opposing α-helix (res. Ala461-Phe476) in the WT simulations. In the variant simulations, the imidazole ring of His575 (in its neutral epsilon protonated form) cannot form the same salt bridges as the guanidinium group of the non-mutated Arg575. Instead, His575 only forms weak hydrogen bonds with the hydroxyl groups of Ser466 and Ser571. Overall, the residue swap has the potential to substantially affect the tertiary structure assembly during the protein folding process.
c.1862G>A	R621Q (3D Viewer)	GAP	Likely Benign		1	6-33440914-G-A	19	1.18e-5	-14.682	Likely Pathogenic	0.910	Likely Pathogenic	Ambiguous	0.621	Likely Pathogenic	0.81	Ambiguous	0.1	1.13	Ambiguous	0.97	Ambiguous	1.35	Destabilizing	-3.98	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	2.82	Benign	0.01	Affected	3.37	35	1	1	1.0	-28.06	243.7	54.3	0.0	0.0	-0.4	0.2		X		X				Potentially Pathogenic	The guanidinium group of Arg621, located in an α helix (res. Glu617-Asn635), forms a salt bridge with Glu525 in a nearby loop and stacks with Leu635. In the variant simulations, the carboxamide side chain of Gln621, which can act as both a hydrogen bond acceptor and donor, also stacks with Leu635 but can only sporadically hydrogen bond with Glu525.Accordingly, the residue swap could affect the tertiary structure integrity by disrupting the salt bridge formation. Additionally, due to its location at the GAP-Ras interface, the residue swap could impact the complex formation with the GTPase, but this cannot be investigated using solvent-only simulations.
c.1730C>G	A577G (3D Viewer)	GAP	Conflicting		2	6-33440782-C-G	1	6.20e-7	-5.717	Likely Benign	0.268	Likely Benign	Likely Benign	0.443	Likely Benign	0.83	Ambiguous	0.0	1.02	Ambiguous	0.93	Ambiguous	0.86	Ambiguous	-1.84	Neutral	0.997	Probably Damaging	0.990	Probably Damaging	-1.31	Pathogenic	0.31	Tolerated	3.37	34	1	0	-2.2	-14.03	158.7	23.6	0.0	0.0	0.0	0.0						X		Potentially Benign	Ala577 is located near the end and outer surface of an α-helix (res. Arg563-Glu578), where its methyl group does not form any particular interactions in the WT simulations. The introduced residue, glycine, is known as an “α-helix breaker.” However, the residue swap caused only minor helix shortening in one of the replica simulations for the variant system. Regardless, the residue swap seems to be well tolerated based on the variant simulations.
c.1018G>A	A340T (3D Viewer)	C2				6-33437923-G-A			-3.286	Likely Benign	0.086	Likely Benign	Likely Benign	0.105	Likely Benign	0.84	Ambiguous	0.2	0.96	Ambiguous	0.90	Ambiguous	-0.54	Ambiguous	0.62	Neutral	0.454	Possibly Damaging	0.192	Benign	1.93	Pathogenic	0.47	Tolerated	3.42	13	0	1	-2.5	30.03
c.1453C>G	R485G (3D Viewer)	GAP				6-33438485-C-G	1	6.20e-7	-15.777	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.631	Likely Pathogenic	0.84	Ambiguous	0.1	1.60	Ambiguous	1.22	Ambiguous	0.98	Ambiguous	-6.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	1.92	Pathogenic	0.00	Affected	3.37	35	-2	-3	4.1	-99.14
c.1761G>T	R587S (3D Viewer)	GAP				6-33440813-G-T	4	2.48e-6	-12.264	Likely Pathogenic	0.830	Likely Pathogenic	Ambiguous	0.508	Likely Pathogenic	0.84	Ambiguous	0.1	1.79	Ambiguous	1.32	Ambiguous	1.17	Destabilizing	-4.84	Deleterious	0.990	Probably Damaging	0.779	Possibly Damaging	-1.20	Pathogenic	0.09	Tolerated	3.37	35	-1	0	3.7	-69.11
c.1893G>C	Q631H (3D Viewer)	GAP				6-33440945-G-C	2	1.24e-6	-13.282	Likely Pathogenic	0.978	Likely Pathogenic	Likely Pathogenic	0.475	Likely Benign	0.84	Ambiguous	0.2	2.21	Destabilizing	1.53	Ambiguous	0.84	Ambiguous	-4.98	Deleterious	0.995	Probably Damaging	0.986	Probably Damaging	2.75	Benign	0.00	Affected	3.37	34	0	3	0.3	9.01
c.1993T>C	Y665H (3D Viewer)	GAP				6-33441252-T-C	2	1.24e-6	-9.303	Likely Pathogenic	0.389	Ambiguous	Likely Benign	0.129	Likely Benign	0.85	Ambiguous	0.0	0.28	Likely Benign	0.57	Ambiguous	1.12	Destabilizing	-2.00	Neutral	1.000	Probably Damaging	0.996	Probably Damaging	3.45	Benign	0.48	Tolerated	3.38	28	2	0	-1.9	-26.03
c.724T>C	W242R (3D Viewer)	PH				6-33435575-T-C	2	1.24e-6	-11.948	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.858	Likely Pathogenic	0.85	Ambiguous	0.5	1.15	Ambiguous	1.00	Ambiguous	1.34	Destabilizing	-12.71	Deleterious	0.995	Probably Damaging	0.854	Possibly Damaging	1.52	Pathogenic	0.00	Affected	3.40	14	-3	2	-3.6	-30.03
c.1729G>A	A577T (3D Viewer)	GAP	Benign		1	6-33440781-G-A	6	3.72e-6	-5.311	Likely Benign	0.322	Likely Benign	Likely Benign	0.427	Likely Benign	0.86	Ambiguous	0.1	0.54	Ambiguous	0.70	Ambiguous	0.54	Ambiguous	-1.47	Neutral	0.999	Probably Damaging	0.987	Probably Damaging	-1.31	Pathogenic	0.47	Tolerated	3.37	34	1	0	-2.5	30.03	191.9	-43.4	0.0	0.0	0.7	0.1						X		Potentially Benign	Ala577 is located near the end and outer surface of an α-helix (res. Arg563-Glu578), where its methyl group does not form any particular interactions in the WT simulations. In the variant simulations, the hydroxyl group of the Thr577 side chain hydrogen bonds with the backbone atoms of Arg573 and Lys574 within the same helix, which has the potential to weaken the stability of the secondary structure element. Regardless, the residue swap seems to be well tolerated based on the variant simulations.
c.1091C>T	P364L (3D Viewer)	C2				6-33437996-C-T			-10.620	Likely Pathogenic	0.457	Ambiguous	Likely Benign	0.387	Likely Benign	0.88	Ambiguous	0.9	-0.73	Ambiguous	0.08	Likely Benign	0.31	Likely Benign	-7.78	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	1.54	Pathogenic	0.18	Tolerated	3.39	20	-3	-3	5.4	16.04
c.1709C>T	A570V (3D Viewer)	GAP				6-33440761-C-T	1	6.22e-7	-13.083	Likely Pathogenic	0.882	Likely Pathogenic	Ambiguous	0.669	Likely Pathogenic	0.88	Ambiguous	0.3	1.63	Ambiguous	1.26	Ambiguous	0.46	Likely Benign	-3.75	Deleterious	0.999	Probably Damaging	0.988	Probably Damaging	-1.30	Pathogenic	0.06	Tolerated	3.37	35	0	0	2.4	28.05
c.1998G>C	E666D (3D Viewer)	GAP	Uncertain		1				-8.820	Likely Pathogenic	0.704	Likely Pathogenic	Likely Benign	0.197	Likely Benign	0.88	Ambiguous	0.0	0.37	Likely Benign	0.63	Ambiguous	1.05	Destabilizing	-2.69	Deleterious	0.992	Probably Damaging	0.603	Possibly Damaging	3.43	Benign	0.06	Tolerated	3.38	28	3	2	0.0	-14.03	237.2	16.5	0.0	0.0	-0.3	0.1		X						Potentially Pathogenic	The carboxylate group of Glu666, located on the α-helix (res. Ser641-Glu666), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), such as Lys566, Thr672, and Asn669, in the WT simulations. In the variant simulations, the shorter side chain of Asp666 cannot maintain these interactions as efficiently as Glu666 in the WT, resulting in a less coordinated hydrogen-bond network.
c.2182C>T	P728S (3D Viewer)	GAP				6-33441647-C-T	1	6.20e-7	-9.047	Likely Pathogenic	0.897	Likely Pathogenic	Ambiguous	0.280	Likely Benign	0.89	Ambiguous	0.0	0.98	Ambiguous	0.94	Ambiguous	0.54	Ambiguous	-6.38	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	0.68	Pathogenic	0.00	Affected	3.59	7	-1	1	0.8	-10.04
c.1130T>C	M377T (3D Viewer)	C2				6-33438035-T-C	5	1.17e-5	-1.881	Likely Benign	0.090	Likely Benign	Likely Benign	0.245	Likely Benign	0.90	Ambiguous	0.4	1.95	Ambiguous	1.43	Ambiguous	0.59	Ambiguous	-0.65	Neutral	0.000	Benign	0.002	Benign	5.47	Benign	0.05	Affected	4.32	12	-1	-1	-2.6	-30.09
c.2047A>G	I683V (3D Viewer)	GAP	Uncertain		1	6-33441306-A-G	2	1.24e-6	-7.588	In-Between	0.138	Likely Benign	Likely Benign	0.112	Likely Benign	0.90	Ambiguous	0.0	0.60	Ambiguous	0.75	Ambiguous	0.76	Ambiguous	-0.78	Neutral	0.538	Possibly Damaging	0.080	Benign	3.35	Benign	0.14	Tolerated	3.42	17	4	3	-0.3	-14.03	215.6	29.1	0.0	0.0	-0.7	0.1						X		Potentially Benign	The sec-butyl side chain of Ile683, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is sterically packed against His453 and Glu688. In the variant simulations, the iso-propyl side chain of Val683 has similar size and physicochemical properties as Ile630 in the WT, and thus, it is able to maintain similar interactions in the inter-helix space. Consequently, no negative structural effects are observed during the simulations due to the residue swap.
c.1153T>C	S385P (3D Viewer)	C2	Uncertain		1	6-33438058-T-C			-5.431	Likely Benign	0.123	Likely Benign	Likely Benign	0.385	Likely Benign	0.91	Ambiguous	0.6	-0.90	Ambiguous	0.01	Likely Benign	0.19	Likely Benign	-0.26	Neutral	0.676	Possibly Damaging	0.693	Possibly Damaging	4.63	Benign	0.04	Affected	4.32	3	1	-1	-0.8	10.04	210.3	18.5	1.8	0.9	0.3	0.0								Uncertain	Ser385 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and so they are rich in glycine residues, prolines, and, to a lesser extent, small hydrophilic residues to ensure maximum flexibility. Thus, the variant’s Pro385 is potentially tolerated in the Ω loop. However, since the effects on Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1129A>G	M377V (3D Viewer)	C2				6-33438034-A-G			-1.507	Likely Benign	0.073	Likely Benign	Likely Benign	0.161	Likely Benign	0.92	Ambiguous	0.3	1.27	Ambiguous	1.10	Ambiguous	0.48	Likely Benign	-0.31	Neutral	0.000	Benign	0.000	Benign	5.46	Benign	0.15	Tolerated	4.32	12	1	2	2.3	-32.06
c.2060G>A	R687Q (3D Viewer)	GAP	Likely Benign		1				-10.002	Likely Pathogenic	0.575	Likely Pathogenic	Likely Benign	0.401	Likely Benign	0.92	Ambiguous	0.1	-0.37	Likely Benign	0.28	Likely Benign	1.55	Destabilizing	-3.37	Deleterious	1.000	Probably Damaging	0.844	Possibly Damaging	3.91	Benign	0.03	Affected	3.42	17	1	1	1.0	-28.06
c.1202G>A	R401Q (3D Viewer)	C2	Uncertain		1	6-33438107-G-A			-11.213	Likely Pathogenic	0.969	Likely Pathogenic	Likely Pathogenic	0.780	Likely Pathogenic	0.96	Ambiguous	0.1	1.50	Ambiguous	1.23	Ambiguous	1.20	Destabilizing	-3.69	Deleterious	0.999	Probably Damaging	0.978	Probably Damaging	5.47	Benign	0.04	Affected	3.38	27	1	1	1.0	-28.06
c.1848T>A	D616E (3D Viewer)	GAP				6-33440900-T-A	1	6.20e-7	-7.250	In-Between	0.695	Likely Pathogenic	Likely Benign	0.092	Likely Benign	0.96	Ambiguous	0.1	1.52	Ambiguous	1.24	Ambiguous	0.58	Ambiguous	-2.85	Deleterious	0.421	Benign	0.232	Benign	3.32	Benign	0.03	Affected	3.37	35	2	3	0.0	14.03
c.1848T>G	D616E (3D Viewer)	GAP				6-33440900-T-G	3	1.86e-6	-7.250	In-Between	0.695	Likely Pathogenic	Likely Benign	0.092	Likely Benign	0.96	Ambiguous	0.1	1.52	Ambiguous	1.24	Ambiguous	0.58	Ambiguous	-2.85	Deleterious	0.421	Benign	0.232	Benign	3.32	Benign	0.03	Affected	3.37	35	2	3	0.0	14.03
c.700C>T	R234W (3D Viewer)	PH	Uncertain		1	6-33435551-C-T	3	1.86e-6	-12.625	Likely Pathogenic	0.947	Likely Pathogenic	Ambiguous	0.805	Likely Pathogenic	0.96	Ambiguous	0.3	0.69	Ambiguous	0.83	Ambiguous	0.13	Likely Benign	-5.52	Deleterious	0.997	Probably Damaging	0.803	Possibly Damaging	5.76	Benign	0.01	Affected	3.40	14	2	-3	3.6	30.03	262.8	39.6	-0.1	0.0	-0.2	0.2		X						Potentially Pathogenic	The guanidinium group of Arg234, located in a β-α loop between an anti-parallel β sheet strand (residues Gly227-Phe231) and an α helix (res. Ala236-Val250), forms a salt bridge with the carboxylate group of Glu238 in the α helix. Occasionally, it also bonds with the GAP domain residues Ser678 and Glu680. Thus, the positively charged Arg234 could contribute to the tertiary structure assembly between the PH and GAP domains. In contrast, the indole side chain of Trp234 in the variant is located on the protein surface in the variant simulations and is unable to form any interactions.
c.1435C>G	R479G (3D Viewer)	GAP				6-33438467-C-G	1	6.20e-7	-8.600	Likely Pathogenic	0.624	Likely Pathogenic	Likely Benign	0.228	Likely Benign	0.97	Ambiguous	0.0	2.51	Destabilizing	1.74	Ambiguous	0.71	Ambiguous	-2.82	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.43	Benign	0.42	Tolerated	3.39	32	-2	-3	4.1	-99.14
c.1625A>G	N542S (3D Viewer)	GAP	Likely Benign		1				-9.675	Likely Pathogenic	0.766	Likely Pathogenic	Likely Benign	0.752	Likely Pathogenic	0.98	Ambiguous	0.1	0.99	Ambiguous	0.99	Ambiguous	0.91	Ambiguous	-4.40	Deleterious	1.000	Probably Damaging	0.989	Probably Damaging	-1.36	Pathogenic	0.13	Tolerated	3.37	35	1	1	2.7	-27.03	212.5	32.1	0.0	0.0	-0.6	0.3		X						Potentially Pathogenic	Asn542 is located in an α-helix (res. Ala533-Val560) next to an α-α loop between two α-helices (res. Gly502-Tyr518 and Ala533-Val560). In the WT simulations, the carboxamide group of the Asn542 side chain forms a hydrogen bond with the backbone carbonyl group of Asn523 and packs favourably against Glu522 from the loop. In contrast, in the variant simulations, the hydroxyl group of the Ser542 side chain is unable to maintain either the hydrogen bond with Asn523 or the packing against the Glu522 side chain. Instead, the hydroxyl group of Ser542 occasionally forms a hydrogen bond with the backbone carbonyl group of Glu538.Altogether, the residue swap results in a looser helix-loop association, which is especially evident in the third replica simulation, where Asn523 moves away from its initial placement next to the α-helix. In short, based on the simulations, the residue swap weakens the GAP domain tertiary structure assembly, which in turn could negatively affect protein folding.
c.794A>C	K265T (3D Viewer)	C2				6-33437699-A-C	1	6.20e-7	-9.425	Likely Pathogenic	0.839	Likely Pathogenic	Ambiguous	0.441	Likely Benign	0.99	Ambiguous	0.1	0.37	Likely Benign	0.68	Ambiguous	0.83	Ambiguous	-3.75	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.91	Pathogenic	0.07	Tolerated	3.38	18	-1	0	3.2	-27.07
c.1428C>G	F476L (3D Viewer)	GAP	Uncertain		2	6-33438460-C-G	4	2.48e-6	-10.109	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.180	Likely Benign	1.00	Ambiguous	0.1	1.04	Ambiguous	1.02	Ambiguous	0.75	Ambiguous	-1.10	Neutral	0.997	Probably Damaging	0.978	Probably Damaging	3.53	Benign	0.60	Tolerated	3.40	22	2	0	1.0	-34.02	235.9	16.1	0.0	0.1	-0.2	0.0	X							Potentially Benign	In the WT simulations, the phenyl ring of Phe476, located at the end of an α-helix (res. Ala461-Phe476), packs with the hydrophobic side chains of Leu482 and Ile483. Additionally, Phe476 stacks with the Arg475 side chain on the preceding α-α loop connecting the two α-helices (res. Ala461-Phe476 and res. Leu489-Glu519) near the GAP-Ras interface.In the variant simulations, Leu476 can maintain hydrophobic packing with neighboring residues, although not as efficiently as the phenylalanine in the WT system. The absence of Phe476/Arg475 stacking weakens the integrity of the α-helix end in the variant simulations. Nonetheless, no large-scale adverse effects are observed in the simulations. Lastly, the potential effect of the residue swap on SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1447A>G	I483V (3D Viewer)	GAP	Uncertain		1				-10.121	Likely Pathogenic	0.523	Ambiguous	Likely Benign	0.228	Likely Benign	1.00	Ambiguous	0.0	0.27	Likely Benign	0.64	Ambiguous	1.02	Destabilizing	-0.86	Neutral	0.914	Possibly Damaging	0.921	Probably Damaging	3.23	Benign	0.03	Affected	3.37	32	3	4	-0.3	-14.03
c.1453C>T	R485C (3D Viewer)	GAP	Uncertain		2	6-33438485-C-T	9	5.58e-6	-14.294	Likely Pathogenic	0.976	Likely Pathogenic	Likely Pathogenic	0.597	Likely Pathogenic	1.00	Ambiguous	0.1	0.26	Likely Benign	0.63	Ambiguous	0.44	Likely Benign	-7.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	1.90	Pathogenic	0.00	Affected	3.37	35	-4	-3	7.0	-53.05	225.5	99.6	-0.1	0.0	-0.3	0.2				X				Uncertain	The guanidinium group of Arg485 is located in a short helical structure (res. Glu480-Leu482) within an α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. The side chain of Arg485 acts as the “arginine finger” of SynGAP, playing a crucial role in Ras-GTPase activation. Consequently, the residue swap inhibits the conversion of GTP to GDP at the enzyme’s active site. Although no negative effects on the protein structure are observed during the simulations, no definite conclusions can be drawn due to the critical role of Arg485 in GTPase activation.
c.1543C>T	R515C (3D Viewer)	GAP				6-33438786-C-T	1	6.20e-7	-10.973	Likely Pathogenic	0.627	Likely Pathogenic	Likely Benign	0.691	Likely Pathogenic	1.00	Ambiguous	0.0	1.13	Ambiguous	1.07	Ambiguous	0.72	Ambiguous	-5.49	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.36	Pathogenic	0.01	Affected	3.37	35	-3	-4	7.0	-53.05
c.600G>C	L200F (3D Viewer)	PH	Uncertain		1	6-33435242-G-C	2	1.24e-6	-7.606	In-Between	0.592	Likely Pathogenic	Likely Benign	0.094	Likely Benign	1.00	Ambiguous	0.5	1.45	Ambiguous	1.23	Ambiguous	0.43	Likely Benign	-1.97	Neutral	0.997	Probably Damaging	0.916	Probably Damaging	4.02	Benign	0.17	Tolerated	3.46	9	2	0	-1.0	34.02	250.4	-15.1	0.6	0.2	0.5	0.0						X		Uncertain	Leu200, a hydrophobic residue located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by another hydrophobic residue, phenylalanine. Both the phenyl group of Phe200 and the branched iso-butyl hydrocarbon sidechain of Leu200 occupy an inward hydrophobic niche (e.g., Leu246, Val222, Phe231) during the simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1497A>C	R499S (3D Viewer)	GAP				6-33438529-A-C	1	6.20e-7	-9.559	Likely Pathogenic	0.935	Likely Pathogenic	Ambiguous	0.632	Likely Pathogenic	1.03	Ambiguous	0.0	2.19	Destabilizing	1.61	Ambiguous	1.40	Destabilizing	-2.69	Deleterious	0.958	Probably Damaging	0.702	Possibly Damaging	-1.43	Pathogenic	0.01	Affected	3.37	35	-1	0	3.7	-69.11
c.1819C>G	L607V (3D Viewer)	GAP	Uncertain		2	6-33440871-C-G	2	1.24e-6	-11.190	Likely Pathogenic	0.637	Likely Pathogenic	Likely Benign	0.715	Likely Pathogenic	1.04	Ambiguous	0.2	1.36	Ambiguous	1.20	Ambiguous	0.90	Ambiguous	-2.99	Deleterious	0.985	Probably Damaging	0.992	Probably Damaging	-1.50	Pathogenic	0.01	Affected	3.37	35	2	1	0.4	-14.03	216.3	28.1	0.1	0.0	0.9	0.2				X				Potentially Benign	Leu607 is located in a short helical region (res. Ser606-Phe608) within an α-α loop connecting two α helices (res. Glu582-Met603 and res. Glu617-Asn635). In the WT simulations, the iso-butyl side chain of Leu607 does not interact with any other residues, but it could potentially interact directly with Ras due to its location at the GAP domain.In the variant simulations, Val607, which has similar size and physicochemical properties to leucine, does not cause any negative effects on the protein structure. However, due to its location at the GAP-Ras interface, the residue swap could affect the complex formation with the GTPase, but this cannot be investigated using solvent-only simulations.
c.1994A>G	Y665C (3D Viewer)	GAP				6-33441253-A-G	1	6.20e-7	-9.007	Likely Pathogenic	0.261	Likely Benign	Likely Benign	0.210	Likely Benign	1.05	Ambiguous	0.1	1.60	Ambiguous	1.33	Ambiguous	1.12	Destabilizing	-3.22	Deleterious	1.000	Probably Damaging	0.981	Probably Damaging	3.45	Benign	0.14	Tolerated	3.38	28	-2	0	3.8	-60.04
c.1658A>C	K553T (3D Viewer)	GAP	Uncertain		1				-15.328	Likely Pathogenic	0.990	Likely Pathogenic	Likely Pathogenic	0.761	Likely Pathogenic	1.06	Ambiguous	0.2	0.48	Likely Benign	0.77	Ambiguous	0.79	Ambiguous	-5.77	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.34	Pathogenic	0.14	Tolerated	3.37	35	0	-1	3.2	-27.07	218.2	-10.7	0.0	0.0	-0.2	0.5		X						Potentially Pathogenic	Lys533 is located on an α-helix (res. Ala533-Val560). In the WT simulations, Lys533 packs against Phe513, and its amino side chain occasionally forms an ionic interaction with the carboxylate group of Glu512 from an opposing α-helix (res. Gln503-Tyr518). In the variant simulations, Thr533 is unable to reproduce these interactions, potentially weakening the integrity of the tertiary structure. Additionally, Thr533 forms a hydrogen bond with the backbone carbonyl group of Leu549 in the same helix, which could potentially weaken the secondary structure. Regardless, the residue swap does not cause significant structural effects based on the simulations.
c.1544G>A	R515H (3D Viewer)	GAP	Uncertain		1	6-33438787-G-A	3	1.86e-6	-10.774	Likely Pathogenic	0.337	Likely Benign	Likely Benign	0.730	Likely Pathogenic	1.07	Ambiguous	0.2	0.74	Ambiguous	0.91	Ambiguous	1.09	Destabilizing	-3.44	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	-1.32	Pathogenic	0.01	Affected	3.37	35	2	0	1.3	-19.05	239.2	77.8	0.0	0.0	0.4	0.2		X						Potentially Benign	The guanidinium group of Arg515, located in the middle of an α-helix at the GAP domain (res. Gly502-Tyr518), forms salt bridges with the carboxylate groups of Glu512 on the same helix and Glu217 on a loop in the PH domain. Additionally, the positively charged Arg515 side chain forms hydrogen bonds with Leu610 and Gln612 in an opposing loop (res. Gly609-Asp616). In contrast, in the variant simulations, the imidazole ring of His515 cannot form salt bridges with either of the acidic residues, and its side chain is too short to form hydrogen bonds with the loop residues. Accordingly, the residue swap could weaken the tertiary structure assembly of the protein. Due to the missing N-terminal part of the SynGAP model, the effect could be largely underestimated or missing. Notably, the doubly protonated and positively charged form of histidine was not simulated here.
c.1855A>T	T619S (3D Viewer)	GAP	Uncertain		1				-8.608	Likely Pathogenic	0.677	Likely Pathogenic	Likely Benign	0.602	Likely Pathogenic	1.09	Ambiguous	0.2	1.35	Ambiguous	1.22	Ambiguous	0.85	Ambiguous	-3.42	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	-1.30	Pathogenic	0.05	Affected	3.37	35	1	1	-0.1	-14.03
c.713A>G	E238G (3D Viewer)	PH				6-33435564-A-G	1	6.19e-7	-12.582	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.889	Likely Pathogenic	1.09	Ambiguous	0.2	3.42	Destabilizing	2.26	Destabilizing	0.87	Ambiguous	-6.35	Deleterious	0.970	Probably Damaging	0.607	Possibly Damaging	5.39	Benign	0.00	Affected	3.40	14	-2	0	3.1	-72.06
c.865A>G	M289V (3D Viewer)	C2	Benign		1				-4.239	Likely Benign	0.117	Likely Benign	Likely Benign	0.150	Likely Benign	1.09	Ambiguous	0.1	-0.27	Likely Benign	0.41	Likely Benign	0.24	Likely Benign	-0.36	Neutral	0.136	Benign	0.054	Benign	1.80	Pathogenic	1.00	Tolerated	3.38	23	2	1	2.3	-32.06	204.2	51.0	0.0	0.0	0.2	0.0						X		Potentially Benign	The hydrophobic residue Met289, located in a β hairpin linking two anti-parallel β sheet strands (res. Met289-Arg299, res. Arg272-Leu286), is swapped for another hydrophobic residue, valine. In the variant simulations, the branched hydrocarbon side chain of Val289 packs against the phenol group of the Tyr291 side chain but is unable to form methionine-aromatic interactions. β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. However, based on the simulations, the residue swap does not cause adverse effects on the structure.
c.916G>A	V306I (3D Viewer)	C2				6-33437821-G-A	11	6.82e-6	-5.989	Likely Benign	0.121	Likely Benign	Likely Benign	0.154	Likely Benign	1.13	Ambiguous	0.2	0.38	Likely Benign	0.76	Ambiguous	0.19	Likely Benign	-0.17	Neutral	0.999	Probably Damaging	0.993	Probably Damaging	1.75	Pathogenic	0.36	Tolerated	3.38	19	3	4	0.3	14.03
c.1309C>T	P437S (3D Viewer)	GAP				6-33438214-C-T	2	1.24e-6	-11.964	Likely Pathogenic	0.518	Ambiguous	Likely Benign	0.226	Likely Benign	1.14	Ambiguous	0.0	-3.31	Stabilizing	-1.09	Ambiguous	0.60	Ambiguous	-6.60	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	3.49	Benign	0.01	Affected	3.38	26	-1	1	0.8	-10.04
c.1760G>C	R587T (3D Viewer)	GAP	Uncertain		1				-9.697	Likely Pathogenic	0.784	Likely Pathogenic	Ambiguous	0.603	Likely Pathogenic	1.14	Ambiguous	0.2	0.74	Ambiguous	0.94	Ambiguous	0.98	Ambiguous	-4.71	Deleterious	0.998	Probably Damaging	0.847	Possibly Damaging	-1.19	Pathogenic	0.08	Tolerated	3.37	35	-1	-1	3.8	-55.08	227.2	87.4	0.0	0.0	0.5	0.1		X						Potentially Pathogenic	The guanidinium group of Arg587, located on an α helix (res. Glu582-Met603), is constantly rotating and breaking/forming multiple hydrogen bonds and/or salt bridges at the surface intersection of α helices in the WT simulations. The positively charged Arg587 side chain can form a salt bridge with either the carboxylate group of Asp583 or Asp586 in the same helix, or with Glu480 on the opposing short helical loop structure (res. Glu480-Leu482).Importantly, the Arg587 side chain also hydrogen bonds with the backbone carbonyl groups of Ala634 and Asn635, as well as the carboxamide group of Asn635 at the end of another α helix (res. Asp616-Phe636). However, in the variant simulations, the neutral hydroxyl group of the Thr587 side chain is unable to form these salt bridges. Due to its smaller size, it also does not form the hydrogen bonds that the Arg587 side chain could. Instead, the hydroxyl group of Thr587 hydrogen bonds with the backbone carbonyl group of Asp583, which could weaken the integrity of the α helix, although this is not observed in the simulations.Overall, the residue swap could weaken the tertiary structure assembly and negatively affect the overall protein folding process.
c.2089T>C	W697R (3D Viewer)	GAP	Likely Benign		1	6-33441348-T-C	1	6.20e-7	-10.020	Likely Pathogenic	0.941	Likely Pathogenic	Ambiguous	0.401	Likely Benign	1.14	Ambiguous	0.1	1.18	Ambiguous	1.16	Ambiguous	1.25	Destabilizing	-9.50	Deleterious	1.000	Probably Damaging	0.994	Probably Damaging	3.45	Benign	0.02	Affected	3.46	13	2	-3	-3.6	-30.03	254.4	-41.2	0.0	0.0	-0.7	0.0						X		Potentially Benign	The indole ring of Trp697, located on the outer surface of an α-helix (res. Leu685-Val699), is not involved in any long-lasting interactions in the WT simulations. In the variant simulations, the positively charged guanidinium side chain of Arg697 occasionally forms hydrogen bonds with nearby residues, such as Ser722 and Asn719. However, similar to Trp697 in the WT, Arg697 does not form any long-lasting interactions and thus does not induce any negative structural effects in the simulations.
c.1480A>G	I494V (3D Viewer)	GAP	Conflicting		2	6-33438512-A-G	36	2.23e-5	-7.102	In-Between	0.112	Likely Benign	Likely Benign	0.439	Likely Benign	1.16	Ambiguous	0.0	0.71	Ambiguous	0.94	Ambiguous	1.02	Destabilizing	-0.83	Neutral	0.278	Benign	0.179	Benign	-1.30	Pathogenic	0.07	Tolerated	3.37	35	4	3	-0.3	-14.03	248.6	29.3	0.0	0.0	-1.1	0.5						X		Potentially Benign	The sec-butyl side chain of Ile494, located in an α-helix (res. Leu489-Glu519), packs against hydrophobic residues (e.g., Phe484, Leu465, Trp572, Ala493, Met468) in an inter-helix space (res. Leu489-Glu519 and res. Ala461-Phe476). In the variant simulations, the hydrophobic iso-propyl side chain of Val494, which is of a similar size and has similar physicochemical properties to Ile494 in the WT, resides similarly in the inter-helix hydrophobic space. Thus, no negative effects on the protein structure are observed.
c.2116G>A	E706K (3D Viewer)	GAP	Uncertain		1				-10.519	Likely Pathogenic	0.833	Likely Pathogenic	Ambiguous	0.080	Likely Benign	1.17	Ambiguous	0.1	0.51	Ambiguous	0.84	Ambiguous	0.08	Likely Benign	-1.51	Neutral	0.345	Benign	0.028	Benign	4.15	Benign	0.52	Tolerated	3.47	10	0	1	-0.4	-0.94	187.1	49.2	0.0	0.0	0.4	0.1						X		Uncertain	The carboxylate side chain of Glu706, located at the end and outer surface of an α-helix (res. Thr704-Gly712), forms a salt bridge with Lys710 and a hydrogen bond with its own backbone amino group at the helix end in the WT simulations. Although Lys706 is unable to make these transient interactions in the variant simulations, there is no apparent negative effect on the protein structure due to the residue swap. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.742C>T	R248W (3D Viewer)	PH	Uncertain		1				-11.647	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.699	Likely Pathogenic	1.17	Ambiguous	0.3	-0.20	Likely Benign	0.49	Likely Benign	0.89	Ambiguous	-6.98	Deleterious	1.000	Probably Damaging	0.948	Probably Damaging	5.62	Benign	0.00	Affected	3.41	14	2	-3	3.6	30.03	266.4	42.3	0.0	0.0	0.3	0.1		X						Potentially Pathogenic	The guanidinium group of Arg248, located on an α helix (res. Ala236-Val250), forms two very stable salt bridges with Asp255 (from a short α helical section, res. Lys254-Asn256) and Glu244 (from a nearby loop) in the WT simulations. In the variant simulations, the indole group of Trp248 cannot form any salt bridges, which could negatively affect the tertiary structure assembly of the PH domain. Instead, in the variant simulations, the indole ring of Trp248 stacks against Pro252, which makes a turn after the α helix.
c.772C>T	R258C (3D Viewer)	C2				6-33437677-C-T	1	6.20e-7	-10.285	Likely Pathogenic	0.790	Likely Pathogenic	Ambiguous	0.771	Likely Pathogenic	1.17	Ambiguous	0.4	1.76	Ambiguous	1.47	Ambiguous	0.87	Ambiguous	-6.79	Deleterious	1.000	Probably Damaging	0.993	Probably Damaging	5.77	Benign	0.00	Affected	3.39	15	-3	-4	7.0	-53.05
c.1861C>G	R621G (3D Viewer)	GAP				6-33440913-C-G	1	6.20e-7	-16.611	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.558	Likely Pathogenic	1.18	Ambiguous	0.3	2.07	Destabilizing	1.63	Ambiguous	1.17	Destabilizing	-6.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.84	Benign	0.01	Affected	3.37	35	-2	-3	4.1	-99.14
c.776G>A	R259Q (3D Viewer)	C2				6-33437681-G-A	1	6.20e-7	-12.598	Likely Pathogenic	0.966	Likely Pathogenic	Likely Pathogenic	0.851	Likely Pathogenic	1.19	Ambiguous	0.3	1.30	Ambiguous	1.25	Ambiguous	1.40	Destabilizing	-3.68	Deleterious	0.999	Probably Damaging	0.978	Probably Damaging	5.81	Benign	0.01	Affected	3.39	15	1	1	1.0	-28.06	258.7	52.8	0.1	0.1	-0.3	0.4	X	X						Potentially Pathogenic	The guanidinium group of Arg259, located at the beginning of an anti-parallel β sheet strand (res. Arg259-Arg272), forms salt bridges with the carboxylate groups of Asp684 at the end of an α helix (res. Ile683-Gln702, GAP domain) and Asp261 on the same β strand. The Arg259 side chain also frequently forms hydrogen bonds with the backbone carbonyl groups of Ser257, Asn256, and Asp255. In the variant simulations, the carboxamide group of the Gln259 side chain cannot form salt bridges or maintain hydrogen bonding with the carboxylate group of Asp684, which could affect the tertiary structure assembly between the C2 and GAP domains. Notably, the amino group of the Lys254 side chain maintains a salt bridge with Asp684 and Glu244 throughout the variant simulations, but this interaction is not maintained in the WT simulations. Thus, the partially or loosely α helical conformation of a lysine-containing loop (res. Lys251-Ser257), which extends to a nearby α helix (res. Met414-Asn426), could be stabilized due to the residue swap.
c.947A>G	N316S (3D Viewer)	C2				6-33437852-A-G	1	6.20e-7	-4.512	Likely Benign	0.148	Likely Benign	Likely Benign	0.151	Likely Benign	1.19	Ambiguous	0.1	0.59	Ambiguous	0.89	Ambiguous	0.68	Ambiguous	-2.22	Neutral	0.999	Probably Damaging	0.992	Probably Damaging	1.77	Pathogenic	0.38	Tolerated	3.38	23	1	1	2.7	-27.03
c.1484A>G	E495G (3D Viewer)	GAP				6-33438516-A-G	1	6.20e-7	-9.400	Likely Pathogenic	0.923	Likely Pathogenic	Ambiguous	0.867	Likely Pathogenic	1.21	Ambiguous	0.0	2.06	Destabilizing	1.64	Ambiguous	0.78	Ambiguous	-6.70	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.46	Pathogenic	0.02	Affected	3.37	35	-2	0	3.1	-72.06
c.1290G>A	M430I (3D Viewer)	GAP				6-33438195-G-A	1	6.19e-7	-4.655	Likely Benign	0.420	Ambiguous	Likely Benign	0.068	Likely Benign	1.22	Ambiguous	0.1	-0.29	Likely Benign	0.47	Likely Benign	0.65	Ambiguous	-1.62	Neutral	0.134	Benign	0.025	Benign	3.54	Benign	0.40	Tolerated	3.37	29	1	2	2.6	-18.03
c.1195G>A	A399T (3D Viewer)	C2	Benign		1				-5.236	Likely Benign	0.114	Likely Benign	Likely Benign	0.272	Likely Benign	1.24	Ambiguous	0.1	0.91	Ambiguous	1.08	Ambiguous	0.49	Likely Benign	-0.40	Neutral	0.131	Benign	0.039	Benign	5.41	Benign	0.69	Tolerated	3.38	26	1	0	-2.5	30.03	211.4	-41.4	0.0	0.0	0.6	0.4		X						Potentially Pathogenic	The methyl group of Ala399, located in an anti-parallel β sheet strand (res. Ala399-Ile411), is swapped for a hydroxyl-containing threonine. In the variant simulations, the hydroxyl group of Thr399 can form H-bonds with the backbone atoms of the residues in the membrane-facing loops (e.g., Gly382) in the C2 domain. Consequently, the ability of the Thr399 side chain to form H-bonds with the membrane-facing loops could adversely affect the dynamics and stability of the SynGAP-membrane association. However, since the effects on the dynamics of the membrane-facing loops can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1606T>G	L536V (3D Viewer)	GAP	Uncertain		1				-9.014	Likely Pathogenic	0.269	Likely Benign	Likely Benign	0.586	Likely Pathogenic	1.25	Ambiguous	0.3	1.22	Ambiguous	1.24	Ambiguous	1.20	Destabilizing	-2.81	Deleterious	0.998	Probably Damaging	0.992	Probably Damaging	-1.34	Pathogenic	0.09	Tolerated	3.37	34	2	1	0.4	-14.03	204.7	26.4	0.2	0.0	-0.2	0.2						X		Potentially Benign	Leu536 is located on an α-helix (res. Ala533-Val560) at the membrane interface. The iso-butyl group of Leu536 interacts with nearby hydrophobic residues in the preceding loop (e.g., Val526, Pro528, Cys531). In the variant simulations, the iso-propyl side chain of Val536 forms similar hydrophobic interactions as Leu536 in the WT, causing no negative structural effects.
c.848A>C	E283A (3D Viewer)	C2				6-33437753-A-C	2	1.24e-6	-12.547	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.529	Likely Pathogenic	1.26	Ambiguous	0.1	1.19	Ambiguous	1.23	Ambiguous	0.53	Ambiguous	-5.52	Deleterious	0.999	Probably Damaging	0.995	Probably Damaging	1.67	Pathogenic	0.01	Affected	3.38	19	-1	0	5.3	-58.04
c.1718G>T	R573L (3D Viewer)	GAP	Likely Pathogenic		1				-13.120	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.833	Likely Pathogenic	1.30	Ambiguous	0.6	1.11	Ambiguous	1.21	Ambiguous	0.80	Ambiguous	-5.74	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.41	Pathogenic	0.01	Affected	3.37	35	-3	-2	8.3	-43.03	237.4	60.7	0.0	0.0	-0.7	0.3	X	X						Potentially Pathogenic	The guanidinium group of Arg573, located in an α-helix (res. Arg563-Glu578), forms a salt bridge with the carboxylate groups of Glu582 and/or Asp586 from a nearby α-helix (res. Glu582-Met603) in the WT simulations. Additionally, the Arg573 side chain stacks planarly with the aromatic phenol ring of Tyr665 and hydrogen bonds with the hydroxyl group of Ser668 from another α-helix (res. Ser641-Ser668). In the variant simulations, the aliphatic iso-butyl group of the Leu573 side chain fails to establish any of these interactions, which, in turn, lowers the integrity of the opposing α-helix end (res. Glu582-Met603). Overall, the residue swap has the potential to substantially affect the tertiary structure assembly during the protein folding process.	10.1016/j.ajhg.2020.11.011
c.913A>G	T305A (3D Viewer)	C2	Uncertain		1	6-33437818-A-G	13	8.05e-6	-4.307	Likely Benign	0.078	Likely Benign	Likely Benign	0.144	Likely Benign	1.30	Ambiguous	0.6	1.55	Ambiguous	1.43	Ambiguous	0.77	Ambiguous	-2.10	Neutral	0.939	Possibly Damaging	0.645	Possibly Damaging	1.76	Pathogenic	0.12	Tolerated	3.40	20	1	0	2.5	-30.03	177.9	43.5	-0.2	0.1	0.4	0.0								Uncertain	The hydroxyl group of Thr305, located at the beginning of an anti-parallel β strand (res. Thr305-Asn315), hydrogen bonds with the carboxylate groups of Glu270 and Asp304 in the anti-parallel β strand and the adjacent β hairpin loop, respectively. In the variant simulations, the methyl group of the Ala305 side chain cannot hydrogen bond with either of the acidic residues, which could weaken the integrity of the tertiary structure and the β hairpin loop. Indeed, the guanidinium group of Arg299 does not acquire its central hairpin loop position due to the residue swap.β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Due to its location near the membrane surface, the residue swap could also affect the C2 loop dynamics and SynGAP-membrane association. However, this is beyond the scope of the solvent-only simulations to unravel.
c.1190G>T	C397F (3D Viewer)	C2				6-33438095-G-T	1	6.20e-7	-6.571	Likely Benign	0.194	Likely Benign	Likely Benign	0.493	Likely Benign	1.31	Ambiguous	1.7	3.61	Destabilizing	2.46	Destabilizing	0.12	Likely Benign	-1.95	Neutral	0.952	Possibly Damaging	0.497	Possibly Damaging	4.65	Benign	0.07	Tolerated	3.41	15	-2	-4	0.3	44.04
c.1742G>A	R581Q (3D Viewer)	GAP	Benign		1	6-33440794-G-A	8	4.96e-6	-7.584	In-Between	0.673	Likely Pathogenic	Likely Benign	0.481	Likely Benign	1.31	Ambiguous	0.1	-0.42	Likely Benign	0.45	Likely Benign	0.88	Ambiguous	-2.77	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	-1.21	Pathogenic	0.11	Tolerated	3.37	34	1	1	1.0	-28.06	239.6	53.5	-0.2	0.2	-0.4	0.1		X						Potentially Pathogenic	Arg581 is located on a short α-α loop between two α helices (res. Arg563-Glu578 and res. Glu582-Ser604). In the WT simulations, the guanidinium group of Arg581 forms salt bridges with the carboxylate groups of Asp583 within the same helix, as well as with Glu478 and/or Glu480 on a slightly α-helical loop (res. Glu478-Thr488) preceding another α helix (res. Ala461-Phe476).In the variant simulations, the neutral carboxamide group of the Gln581 side chain cannot form any of these salt bridges. Instead, it packs hydrophobically against Met477 and Ile587 or forms hydrogen bonds sporadically with nearby residues (e.g., Asp583, Arg587). Thus, although no drastic changes are observed in the variant simulations, the residue swap could weaken the tertiary structure assembly.
c.1741C>T	R581W (3D Viewer)	GAP	Uncertain		2				-12.855	Likely Pathogenic	0.920	Likely Pathogenic	Ambiguous	0.678	Likely Pathogenic	1.32	Ambiguous	0.1	-0.32	Likely Benign	0.50	Ambiguous	0.68	Ambiguous	-6.79	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	-1.37	Pathogenic	0.01	Affected	3.37	34	2	-3	3.6	30.03	257.8	36.0	0.1	0.1	0.1	0.3	X	X						Potentially Pathogenic	Arg581 is located on a short α-α loop between two α helices (res. Arg563-Glu578 and res. Glu582-Ser604). In the WT simulations, the guanidinium group of Arg581 forms salt bridges with the carboxylate groups of Asp583 within the same helix, as well as with Glu478 and/or Glu480 in a slightly α-helical loop (res. Glu478-Thr488) preceding another α helix (res. Ala461-Phe476).In the variant simulations, the neutral indole ring of the Trp581 side chain cannot form any of these salt bridges. Instead, it packs hydrophobically against Met477 and Ile587 without forming any direct hydrogen bonds. The tendency of the loop (res. Asp477-Thr488) to acquire an α-helical structure seems to marginally increase, potentially due to Trp581's inability to coordinate stable hydrogen bonds with the loop residues (e.g., Glu478-Arg581 salt bridge). Additionally, the residue swap could weaken the tertiary structure assembly and negatively affect the overall protein folding process.
c.1888A>G	I630V (3D Viewer)	GAP	Benign/Likely benign		4	6-33440940-A-G	59	3.66e-5	-7.264	In-Between	0.144	Likely Benign	Likely Benign	0.143	Likely Benign	1.33	Ambiguous	0.0	0.94	Ambiguous	1.14	Ambiguous	0.64	Ambiguous	-0.38	Neutral	0.018	Benign	0.011	Benign	-1.37	Pathogenic	0.35	Tolerated	3.37	34	4	3	-0.3	-14.03	235.0	26.2	-0.1	0.0	-0.3	0.1						X		Potentially Benign	The sec-butyl side chain of Ile630, located in an α helix (res. Glu617-Asn635), packs with hydrophobic residues (e.g., Phe594, Leu633, Ile626, Ile602) in the hydrophobic inter-helix space between two α helices (res. Glu617-Asn635 and res. Glu582-Met603).In the variant simulations, the iso-propyl side chain of Val630, which shares a similar size and physicochemical properties with Ile630 in the WT, maintains similar interactions in the inter-helix space. Although no negative structural effects are observed during the simulations, the implications of the residue swap on the complex formation with the GTPase, due to its location, cannot be investigated using solvent-only simulations.
c.1964T>C	L655P (3D Viewer)	GAP				6-33441223-T-C	1	6.20e-7	-9.771	Likely Pathogenic	0.982	Likely Pathogenic	Likely Pathogenic	0.126	Likely Benign	1.33	Ambiguous	0.5	6.52	Destabilizing	3.93	Destabilizing	0.57	Ambiguous	-1.36	Neutral	0.981	Probably Damaging	0.772	Possibly Damaging	3.47	Benign	0.32	Tolerated	3.39	24	-3	-3	-5.4	-16.04
c.2101C>T	P701S (3D Viewer)	GAP	Uncertain		1	6-33441360-C-T	3	1.86e-6	-4.375	Likely Benign	0.221	Likely Benign	Likely Benign	0.132	Likely Benign	1.33	Ambiguous	0.0	0.12	Likely Benign	0.73	Ambiguous	-0.36	Likely Benign	0.78	Neutral	0.044	Benign	0.025	Benign	3.48	Benign	1.00	Tolerated	3.47	10	-1	1	0.8	-10.04																10.1016/j.ajhg.2020.11.011
c.953C>T	P318L (3D Viewer)	C2	Uncertain		3	6-33437858-C-T	3	1.86e-6	-10.090	Likely Pathogenic	0.958	Likely Pathogenic	Likely Pathogenic	0.624	Likely Pathogenic	1.33	Ambiguous	0.1	0.26	Likely Benign	0.80	Ambiguous	0.43	Likely Benign	-8.96	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.82	Pathogenic	0.03	Affected	3.38	23	-3	-3	5.4	16.04	228.6	-68.9	-0.7	0.7	-0.4	0.1						X		Potentially Benign	The cyclic five-membered pyrrolidine ring of Pro318, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Asp330-Ala322, res. Thr305-Asn315), packs against the hydrophobic side chain of Ile205 at the end of the anti-parallel β sheet in the PH domain. In the variant simulations, the iso-butyl side chain of Leu318 is unable to do the same, potentially weakening the PH and C2 domain association. Importantly, the residue swap could also affect loop formation during folding, as proline can make tighter turns than leucine. Because the residue swap could affect the C2 domain stability, it could also negatively impact the SynGAP-membrane association.
c.1090C>T	P364S (3D Viewer)	C2				6-33437995-C-T	1	6.20e-7	-8.318	Likely Pathogenic	0.214	Likely Benign	Likely Benign	0.307	Likely Benign	1.34	Ambiguous	0.3	0.68	Ambiguous	1.01	Ambiguous	0.83	Ambiguous	-5.98	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	1.62	Pathogenic	0.05	Affected	3.39	20	-1	1	0.8	-10.04
c.1772C>T	A591V (3D Viewer)	GAP				6-33440824-C-T	2	1.24e-6	-12.282	Likely Pathogenic	0.926	Likely Pathogenic	Ambiguous	0.321	Likely Benign	1.35	Ambiguous	0.4	0.98	Ambiguous	1.17	Ambiguous	0.86	Ambiguous	-3.79	Deleterious	0.970	Probably Damaging	0.373	Benign	3.35	Benign	0.02	Affected	3.37	35	0	0	2.4	28.05
c.836G>A	R279Q (3D Viewer)	C2				6-33437741-G-A	6	3.72e-6	-8.730	Likely Pathogenic	0.760	Likely Pathogenic	Likely Benign	0.554	Likely Pathogenic	1.37	Ambiguous	0.1	0.88	Ambiguous	1.13	Ambiguous	1.35	Destabilizing	-2.61	Deleterious	0.999	Probably Damaging	0.994	Probably Damaging	1.94	Pathogenic	0.06	Tolerated	3.39	18	1	1	1.0	-28.06
c.877C>T	R293C (3D Viewer)	C2	Uncertain		1	6-33437782-C-T	3	1.86e-6	-12.844	Likely Pathogenic	0.985	Likely Pathogenic	Likely Pathogenic	0.579	Likely Pathogenic	1.38	Ambiguous	0.1	0.62	Ambiguous	1.00	Ambiguous	0.02	Likely Benign	-7.35	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.46	Pathogenic	0.00	Affected	3.38	23	-4	-3	7.0	-53.05	226.0	96.5	0.0	0.0	0.1	0.1		X		X			X	Potentially Pathogenic	The guanidinium group of the Arg293 side chain, located in an anti-parallel β sheet strand (res. Met289-Pro298), packs against the phenol ring of the Tyr281 side chain or forms a salt bridge with the carboxylate group of Glu283 on the outer side of the C2 domain. The positively charged guanidinium side chain of arginine is on the outside surface of the hydrophobic C2 domain, resulting in a twist in the β strand. Although this twist is maintained in the variant simulations, replacing the positively charged residue with a more hydrophobic one, such as cysteine, could remove the twist during protein folding.Because Arg293 is positioned at the C2 and PH domain interface, the residue swap could significantly impact the tertiary structure assembly. Notably, Arg293 is located at the SynGAP-Ras interface, and its role in complex formation cannot be fully understood through solvent-only simulations.
c.892C>T	P298S (3D Viewer)	C2	Benign		1	6-33437797-C-T	5	3.10e-6	-6.342	Likely Benign	0.144	Likely Benign	Likely Benign	0.189	Likely Benign	1.38	Ambiguous	0.2	1.41	Ambiguous	1.40	Ambiguous	0.58	Ambiguous	-1.20	Neutral	0.991	Probably Damaging	0.898	Possibly Damaging	2.03	Pathogenic	0.85	Tolerated	3.39	20	-1	1	0.8	-10.04
c.979C>G	L327V (3D Viewer)	C2				6-33437884-C-G	3	1.86e-6	-8.978	Likely Pathogenic	0.148	Likely Benign	Likely Benign	0.208	Likely Benign	1.38	Ambiguous	0.1	0.67	Ambiguous	1.03	Ambiguous	1.31	Destabilizing	-1.87	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	2.66	Benign	0.13	Tolerated	3.38	23	1	2	0.4	-14.03
c.1485A>C	E495D (3D Viewer)	GAP	Conflicting		2				-3.574	Likely Benign	0.958	Likely Pathogenic	Likely Pathogenic	0.566	Likely Pathogenic	1.39	Ambiguous	0.1	1.03	Ambiguous	1.21	Ambiguous	0.98	Ambiguous	-2.52	Deleterious	0.998	Probably Damaging	0.989	Probably Damaging	-1.41	Pathogenic	0.17	Tolerated	3.37	35	3	2	0.0	-14.03	220.6	38.8	0.0	0.0	0.1	0.1		X		X				Uncertain	Glu495 is located in the α-helix (res. Leu489-Glu519), and its carboxylate group forms salt bridges with the neighboring Lys492 and with Arg596 on an opposing α-helix (res. Glu582-Met603) in the WT simulations. In the variant simulations, the acidic carboxylate side chain of Asp495 can also form salt bridges with both Lys492 and Arg596. However, the shorter side chain of aspartate tends to favor forming a salt bridge with the nearby Arg499 on the same α-helix instead. Asp495 might not maintain the salt bridge with Arg596 on the opposing α-helix as efficiently as Glu495 in the WT, potentially weakening the tertiary structure. Regardless, the potential negative effect is likely to be minor, with no deleterious effects observed on the protein structure during the simulations. However, due to its location at the GAP-Ras interface, the effect of the residue swap on SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1540A>G	I514V (3D Viewer)	GAP				6-33438783-A-G	7	4.34e-6	-5.187	Likely Benign	0.245	Likely Benign	Likely Benign	0.173	Likely Benign	1.39	Ambiguous	0.0	0.44	Likely Benign	0.92	Ambiguous	0.89	Ambiguous	-0.79	Neutral	0.914	Possibly Damaging	0.960	Probably Damaging	3.15	Benign	0.13	Tolerated	3.37	35	3	4	-0.3	-14.03
c.1723C>T	R575C (3D Viewer)	GAP	Conflicting		3	6-33440775-C-T	23	1.43e-5	-11.179	Likely Pathogenic	0.630	Likely Pathogenic	Likely Benign	0.715	Likely Pathogenic	1.39	Ambiguous	0.2	0.50	Ambiguous	0.95	Ambiguous	0.73	Ambiguous	-5.43	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.30	Pathogenic	0.02	Affected	3.37	35	-4	-3	7.0	-53.05	227.7	99.2	0.0	0.0	0.0	0.1		X						Potentially Pathogenic	The guanidinium group of Arg575, located in an α-helix (res. Arg563-Glu578), forms salt bridges with the carboxylate groups of Asp463 and Asp467, and it also hydrogen bonds with the hydroxyl group of Ser466 on an opposing α-helix (res. Ala461-Phe476) in the WT simulations. In the variant simulations, the thiol group of the Cys575 side chain, which is neither positively charged nor particularly hydrophilic, packs against the hydrophobic Met470 on an opposing α-helix (res. Ala461-Arg475). Additionally, although the thiol group is not an effective hydrogen bonder, the Cys575 side chain rotates to hydrogen bond with the backbone carbonyl group of Ser571 in the same α-helix, which could theoretically lower the helix integrity. Overall, the residue swap has the potential to substantially affect the tertiary structure assembly during the protein folding process.
c.1256A>G	E419G (3D Viewer)	GAP	Uncertain		1				-10.589	Likely Pathogenic	0.956	Likely Pathogenic	Likely Pathogenic	0.469	Likely Benign	1.41	Ambiguous	0.0	1.94	Ambiguous	1.68	Ambiguous	0.83	Ambiguous	-6.42	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	3.31	Benign	0.02	Affected	3.37	29	0	-2	3.1	-72.06	165.3	110.8	0.0	0.0	-0.1	0.0		X						Potentially Pathogenic	The carboxylate group of Glu419, located on an α helix (res. Met414-Glu436), forms a salt bridge with the side chain of either Arg716 or Lys418 from an opposing helix (res. Pro713-Arg726). The backbone amide group of Glu419 does not form H-bonds, resulting in a slight bend in the α helix. Thus, although glycine is known as an “α helix breaker,” the residue swap does not disrupt the continuity or integrity of the α helix. However, because Gly419 cannot form a salt bridge with the guanidinium group of the Arg716 side chain, the C2-GAP domain tertiary structure could be compromised during folding.
c.826C>G	P276A (3D Viewer)	C2				6-33437731-C-G	5	3.10e-6	-3.414	Likely Benign	0.058	Likely Benign	Likely Benign	0.187	Likely Benign	1.42	Ambiguous	0.1	1.01	Ambiguous	1.22	Ambiguous	0.50	Likely Benign	-2.31	Neutral	0.044	Benign	0.030	Benign	1.98	Pathogenic	0.57	Tolerated	3.38	19	-1	1	3.4	-26.04
c.1735C>G	R579G (3D Viewer)	GAP				6-33440787-C-G	1	6.20e-7	-14.298	Likely Pathogenic	0.948	Likely Pathogenic	Ambiguous	0.680	Likely Pathogenic	1.43	Ambiguous	0.0	2.36	Destabilizing	1.90	Ambiguous	1.32	Destabilizing	-5.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.40	Pathogenic	0.01	Affected	3.37	34	-2	-3	4.1	-99.14
c.1423C>T	R475W (3D Viewer)	GAP	Uncertain		1	6-33438455-C-T	1	6.20e-7	-13.235	Likely Pathogenic	0.962	Likely Pathogenic	Likely Pathogenic	0.725	Likely Pathogenic	1.44	Ambiguous	0.4	-0.92	Ambiguous	0.26	Likely Benign	0.56	Ambiguous	-7.56	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	-1.45	Pathogenic	0.00	Affected	3.39	28	2	-3	3.6	30.03	266.9	39.6	0.0	0.0	0.0	0.1	X	X		X				Potentially Pathogenic	In the WT simulations, the guanidinium group of Arg475, located near the end of an α-helix (res. Ala461-Phe476), stacks with the phenyl ring of Phe476 and forms a salt bridge with Glu472. Additionally, Arg475 occasionally forms another salt bridge with the carboxylate group of Glu486 on the α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. Therefore, Arg475 potentially plays a key role in positioning the loop by interacting with Glu486, which is necessary for the positioning of the “arginine finger” (Arg485) and, ultimately, for RasGTPase activation.In the variant simulations, Trp475 moves and stacks with Arg479 on the proceeding α-α loop, disrupting the terminal end of the α-helix. Lastly, the potential effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.907G>A	G303R (3D Viewer)	C2				6-33437812-G-A	1	6.20e-7	-7.493	In-Between	0.724	Likely Pathogenic	Likely Benign	0.048	Likely Benign	1.44	Ambiguous	0.4	0.23	Likely Benign	0.84	Ambiguous	0.73	Ambiguous	-1.38	Neutral	0.001	Benign	0.003	Benign	3.99	Benign	0.06	Tolerated	3.55	18	-2	-3	-4.1	99.14
c.1833G>A	M611I (3D Viewer)	GAP				6-33440885-G-A	1	6.19e-7	-8.552	Likely Pathogenic	0.736	Likely Pathogenic	Likely Benign	0.292	Likely Benign	1.45	Ambiguous	0.4	1.36	Ambiguous	1.41	Ambiguous	0.72	Ambiguous	-2.10	Neutral	0.250	Benign	0.091	Benign	-1.14	Pathogenic	0.38	Tolerated	3.37	35	1	2	2.6	-18.03
c.1226T>G	M409R (3D Viewer)	C2				6-33438131-T-G			-12.795	Likely Pathogenic	0.911	Likely Pathogenic	Ambiguous	0.485	Likely Benign	1.47	Ambiguous	0.4	0.44	Likely Benign	0.96	Ambiguous	1.30	Destabilizing	-4.39	Deleterious	0.877	Possibly Damaging	0.807	Possibly Damaging	4.15	Benign	0.27	Tolerated	3.38	28	-1	0	-6.4	24.99
c.1193C>T	P398L (3D Viewer)	C2	Uncertain		1	6-33438098-C-T	8	4.96e-6	-7.518	In-Between	0.547	Ambiguous	Likely Benign	0.599	Likely Pathogenic	1.48	Ambiguous	0.2	-0.54	Ambiguous	0.47	Likely Benign	0.62	Ambiguous	-7.10	Deleterious	0.961	Probably Damaging	0.256	Benign	5.72	Benign	0.01	Affected	3.40	16	-3	-3	5.4	16.04	245.8	-68.6	-0.1	0.0	-0.3	0.2							X	Potentially Pathogenic	Pro398 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. Although the residue swap does not influence the nearby secondary structure elements, proline is often found at the ends of β sheets due to its disfavored status during folding.Additionally, the Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone. Ω loops are known to play significant roles in protein functions that require flexibility, and thus hydrophobic residues like leucine are rarely tolerated. Although no negative structural effects are visualized in the variant’s simulations, Leu398 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. Since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.2122C>T	L708F (3D Viewer)	GAP				6-33441587-C-T	2	1.24e-6	-9.154	Likely Pathogenic	0.436	Ambiguous	Likely Benign	0.110	Likely Benign	1.48	Ambiguous	0.3	0.93	Ambiguous	1.21	Ambiguous	0.37	Likely Benign	-2.46	Neutral	0.931	Possibly Damaging	0.326	Benign	3.29	Benign	0.07	Tolerated	3.50	9	0	2	-1.0	34.02
c.653T>G	F218C (3D Viewer)	PH				6-33435295-T-G	1	6.20e-7	-7.234	In-Between	0.948	Likely Pathogenic	Ambiguous	0.744	Likely Pathogenic	1.49	Ambiguous	0.1	2.20	Destabilizing	1.85	Ambiguous	1.02	Destabilizing	-4.92	Deleterious	0.994	Probably Damaging	0.667	Possibly Damaging	5.78	Benign	0.03	Affected	3.41	13	-2	-4	-0.3	-44.04
c.970C>T	R324W (3D Viewer)	C2	Uncertain		1	6-33437875-C-T	2	1.24e-6	-12.906	Likely Pathogenic	0.694	Likely Pathogenic	Likely Benign	0.481	Likely Benign	1.49	Ambiguous	0.3	0.56	Ambiguous	1.03	Ambiguous	0.66	Ambiguous	-3.12	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.82	Pathogenic	0.16	Tolerated	3.39	22	2	-3	3.6	30.03	256.6	39.1	0.0	0.1	0.3	0.2		X						Potentially Pathogenic	The guanidinium group of Arg324, located at the end of an anti-parallel β sheet strand (res. Ala322-Asp330), faces outward and frequently forms a salt bridge with the carboxylate group of the Asp288 side chain, which is part of a β strand end (res. Met289-Pro298). In the variant simulations, the indole ring of the Trp324 side chain cannot maintain a similar interaction with the negatively charged carboxylate side chain of Asp288, potentially compromising the folding of the anti-parallel β sheet assembly. However, the residue swap does not appear to negatively impact the protein structure or its integrity based on the simulations.
c.1828C>A	L610I (3D Viewer)	GAP				6-33440880-C-A	1	6.19e-7	-6.362	Likely Benign	0.389	Ambiguous	Likely Benign	0.544	Likely Pathogenic	1.50	Ambiguous	0.2	0.18	Likely Benign	0.84	Ambiguous	0.76	Ambiguous	-1.86	Neutral	0.992	Probably Damaging	0.997	Probably Damaging	-1.34	Pathogenic	0.15	Tolerated	3.37	35	2	2	0.7	0.00
c.745G>A	A249T (3D Viewer)	PH	Uncertain		1				-3.564	Likely Benign	0.805	Likely Pathogenic	Ambiguous	0.487	Likely Benign	1.50	Ambiguous	0.6	1.39	Ambiguous	1.45	Ambiguous	0.30	Likely Benign	-0.96	Neutral	0.990	Probably Damaging	0.815	Possibly Damaging	5.65	Benign	0.40	Tolerated	3.39	15	1	0	-2.5	30.03	214.5	-43.3	0.0	0.0	0.5	0.2						X		Potentially Benign	The methyl group of Ala249, located on the surface of an α helix (res. Ala236-Val250) facing an anti-parallel β sheet strand (res. Ile205-Val209), packs against nearby hydrophobic residues such as Leu200, Leu246, and Val250. In the variant simulations, the hydroxyl group of Thr249, which is not suitable for hydrophobic packing, forms a stable hydrogen bond with the backbone carbonyl of Asn245 in the same helix. Although this interaction could theoretically weaken the structural integrity of the α helix, this destabilizing effect is not observed in the variant simulations.
c.1787G>T	R596L (3D Viewer)	GAP	Uncertain		1				-13.197	Likely Pathogenic	0.992	Likely Pathogenic	Likely Pathogenic	0.756	Likely Pathogenic	1.51	Ambiguous	0.3	-0.58	Ambiguous	0.47	Likely Benign	-0.02	Likely Benign	-6.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.45	Pathogenic	0.00	Affected	3.37	35	-3	-2	8.3	-43.03	234.2	63.4	-0.1	0.0	-0.5	0.6		X		X				Potentially Pathogenic	The guanidinium group of Arg596, located in an α helix (res. Glu582-Met603), forms a salt bridge with the carboxylate group of Glu495 from another α helix (res. Leu489-Glu519). In the WT simulations, the side chain of Arg596 hydrogen bonds with the backbone carbonyl groups of Asn487, Glu486, Arg485, and Phe484. Additionally, Arg596 can hydrogen bond with the carboxamide group of the Asn487 side chain on an opposing loop that links two α helices (res. Ala461-Arg475, res. Leu489-Glu519).However, in the variant simulations, the branched hydrocarbon side chain of Leu596 cannot form any of the hydrogen bonds or salt bridges maintained by the considerably bulkier and positively charged Arg596 side chain. Instead, Leu596 packs hydrophobically with the phenyl ring of Phe484 in the linker loop or residues from the opposing helix (e.g., Ile494, Thr491).Thus, the residue swap could affect the tertiary structure assembly more profoundly than observed in the simulations. Notably, Arg596 plays a key role in positioning the aforementioned loop, which is crucial for the placement of the “arginine finger” or the Arg485 side chain during RasGTPase activation.	10.1016/j.ajhg.2020.11.011
c.1103C>T	P368L (3D Viewer)	C2				6-33438008-C-T	1	6.33e-7	-6.520	Likely Benign	0.444	Ambiguous	Likely Benign	0.248	Likely Benign	1.52	Ambiguous	0.7	1.15	Ambiguous	1.34	Ambiguous	0.52	Ambiguous	-6.61	Deleterious	0.991	Probably Damaging	0.831	Possibly Damaging	1.77	Pathogenic	0.00	Affected	3.42	19	-3	-3	5.4	16.04
c.1474A>G	K492E (3D Viewer)	GAP	Conflicting		2				-16.175	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.510	Likely Pathogenic	1.53	Ambiguous	0.1	1.90	Ambiguous	1.72	Ambiguous	1.42	Destabilizing	-3.98	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.99	Benign	0.01	Affected	3.37	35	1	0	0.4	0.94
c.1495A>G	R499G (3D Viewer)	GAP				6-33438527-A-G	3	1.86e-6	-9.960	Likely Pathogenic	0.789	Likely Pathogenic	Ambiguous	0.681	Likely Pathogenic	1.55	Ambiguous	0.1	2.75	Destabilizing	2.15	Destabilizing	1.41	Destabilizing	-4.50	Deleterious	0.958	Probably Damaging	0.769	Possibly Damaging	-1.47	Pathogenic	0.01	Affected	3.37	35	-2	-3	4.1	-99.14
c.1636T>G	C546G (3D Viewer)	GAP				6-33438879-T-G	1	6.20e-7	-14.026	Likely Pathogenic	0.977	Likely Pathogenic	Likely Pathogenic	0.877	Likely Pathogenic	1.55	Ambiguous	0.0	2.43	Destabilizing	1.99	Ambiguous	1.53	Destabilizing	-9.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.26	Pathogenic	0.06	Tolerated	3.37	35	-3	-3	-2.9	-46.09
c.1759A>G	R587G (3D Viewer)	GAP				6-33440811-A-G	2	1.24e-6	-13.780	Likely Pathogenic	0.780	Likely Pathogenic	Likely Benign	0.578	Likely Pathogenic	1.55	Ambiguous	0.2	2.43	Destabilizing	1.99	Ambiguous	1.55	Destabilizing	-6.07	Deleterious	1.000	Probably Damaging	0.972	Probably Damaging	-1.28	Pathogenic	0.07	Tolerated	3.37	35	-2	-3	4.1	-99.14
c.844T>A	C282S (3D Viewer)	C2	Uncertain		1				-11.846	Likely Pathogenic	0.958	Likely Pathogenic	Likely Pathogenic	0.460	Likely Benign	1.55	Ambiguous	0.1	1.23	Ambiguous	1.39	Ambiguous	1.62	Destabilizing	-9.19	Deleterious	0.997	Probably Damaging	0.994	Probably Damaging	1.64	Pathogenic	0.03	Affected	3.39	18	0	-1	-3.3	-16.06	233.2	14.8	-0.1	0.0	-0.2	0.3						X		Potentially Benign	The thiol-containing side chain of Cys282, located at the beginning of an anti-parallel β sheet strand (res. Arg279-Leu286), packs against multiple hydrophobic residues (e.g., Ile268, Leu284, Trp308, Leu327). In the variant simulations, the hydroxyl-containing side chain of Ser282 is more hydrophilic and, hence, not as favorable as Cys282 for this hydrophobic niche. Due to this polarity difference, the residue swap could potentially weaken the hydrophobic packing of the C2 domain during the folding process.Moreover, because the C2 domain interacts with the membrane, there could also be a negative effect on the stability of the SynGAP-membrane association. However, no large-scale structural changes were observed during the variant simulations. The hydroxyl group of Ser282 forms a hydrogen bond with the backbone carbonyl group of His326 in another β strand (res. Ala322-Arg329), which competes directly with the backbone amide group of Glu283 within the secondary structure element.
c.626T>C	V209A (3D Viewer)	PH				6-33435268-T-C	1	6.20e-7	-9.796	Likely Pathogenic	0.976	Likely Pathogenic	Likely Pathogenic	0.236	Likely Benign	1.56	Ambiguous	0.3	1.85	Ambiguous	1.71	Ambiguous	1.60	Destabilizing	-2.79	Deleterious	0.958	Probably Damaging	0.581	Possibly Damaging	3.70	Benign	0.02	Affected	3.41	13	0	0	-2.4	-28.05
c.1997A>G	E666G (3D Viewer)	GAP	Likely Benign		1	6-33441256-A-G	10	6.20e-6	-12.261	Likely Pathogenic	0.911	Likely Pathogenic	Ambiguous	0.522	Likely Pathogenic	1.57	Ambiguous	0.1	1.46	Ambiguous	1.52	Ambiguous	0.93	Ambiguous	-6.25	Deleterious	1.000	Probably Damaging	0.970	Probably Damaging	3.37	Benign	0.02	Affected	3.38	28	0	-2	3.1	-72.06	173.9	98.5	0.0	0.0	-0.7	0.0		X						Potentially Pathogenic	In the WT simulations, the carboxylate group of Glu666, located on the α-helix (res. Ser641-Glu666), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), such as Lys566, Thr672, and Asn669. In the variant simulations, the carbonyl group of Gly666 occasionally forms hydrogen bonds with Lys566 and Asn669. However, Gly666 lacks a side chain and thus cannot maintain as well-coordinated a hydrogen-bond network as Glu666 in the WT, which may affect the tertiary structure assembly.
c.1201C>T	R401W (3D Viewer)	C2				6-33438106-C-T	2	1.24e-6	-10.712	Likely Pathogenic	0.990	Likely Pathogenic	Likely Pathogenic	0.711	Likely Pathogenic	1.59	Ambiguous	0.2	1.04	Ambiguous	1.32	Ambiguous	0.73	Ambiguous	-7.34	Deleterious	1.000	Probably Damaging	0.993	Probably Damaging	5.40	Benign	0.00	Affected	3.38	27	-3	2	3.6	30.03
c.773G>A	R258H (3D Viewer)	C2	Benign/Likely benign		3	6-33437678-G-A	10	6.20e-6	-10.533	Likely Pathogenic	0.525	Ambiguous	Likely Benign	0.830	Likely Pathogenic	1.60	Ambiguous	0.6	1.00	Ambiguous	1.30	Ambiguous	1.47	Destabilizing	-4.06	Deleterious	1.000	Probably Damaging	0.991	Probably Damaging	5.77	Benign	0.01	Affected	3.39	15	2	0	1.3	-19.05	212.5	81.8	0.1	0.0	-0.5	0.2		X						Potentially Pathogenic	The guanidinium group of Arg258, located at the end of an α-β loop connecting the PH domain to the C2 domain (res. Lys251-Arg258), forms hydrogen bonds with the carboxamide groups of Asn727 and Asn729 side chains, as well as with the backbone carbonyl groups of Ala724, Leu725, and Asn727 in the WT simulations. Although the imidazole group of His258 can act as a hydrogen bond donor/acceptor, the swapped residue is unable to maintain an equally well-coordinated hydrogen bond network for linking the C2 and GAP domains in the variant simulations.
c.1771G>A	A591T (3D Viewer)	GAP	Conflicting		3	6-33440823-G-A	18	1.12e-5	-9.572	Likely Pathogenic	0.704	Likely Pathogenic	Likely Benign	0.270	Likely Benign	1.61	Ambiguous	0.2	1.00	Ambiguous	1.31	Ambiguous	1.19	Destabilizing	-3.40	Deleterious	0.955	Possibly Damaging	0.209	Benign	3.48	Benign	0.01	Affected	3.37	35	1	0	-2.5	30.03	202.9	-43.4	0.2	0.0	0.7	0.1						X		Potentially Benign	The methyl group of the Ala591 side chain, located in the middle of an α helix (res. Glu582-Met603), packs against hydrophobic residues (e.g., Ile483, Phe484) of an opposing partially helical loop (res. Phe476-Asn487).In the variant simulations, the hydroxyl group of Thr591 can form hydrogen bonds with the backbone carbonyl of Ile843 in the opposing loop or the backbone carbonyl group of Arg587. These interactions could either reinforce the tertiary assembly or weaken the α helix unity. Additionally, the Thr591 side chain can hydrogen bond with the guanidinium group of the Arg587 side chain, potentially strengthening the α helix unity.Overall, the residue swap does not seem to cause any major negative effects on the protein structure.
c.1430T>C	M477T (3D Viewer)	GAP				6-33438462-T-C	2	1.24e-6	-2.509	Likely Benign	0.372	Ambiguous	Likely Benign	0.273	Likely Benign	1.62	Ambiguous	0.2	0.16	Likely Benign	0.89	Ambiguous	0.51	Ambiguous	-1.33	Neutral	0.765	Possibly Damaging	0.363	Benign	-1.10	Pathogenic	0.40	Tolerated	3.37	34	-1	-1	-2.6	-30.09
c.1024T>C	Y342H (3D Viewer)	C2				6-33437929-T-C	1	6.20e-7	-6.459	Likely Benign	0.944	Likely Pathogenic	Ambiguous	0.453	Likely Benign	1.63	Ambiguous	0.1	1.33	Ambiguous	1.48	Ambiguous	0.73	Ambiguous	-3.61	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.72	Pathogenic	0.06	Tolerated	3.37	25	2	0	-1.9	-26.03
c.1429A>G	M477V (3D Viewer)	GAP				6-33438461-A-G	1	6.20e-7	-3.995	Likely Benign	0.127	Likely Benign	Likely Benign	0.209	Likely Benign	1.64	Ambiguous	0.3	0.42	Likely Benign	1.03	Ambiguous	0.24	Likely Benign	-1.04	Neutral	0.716	Possibly Damaging	0.204	Benign	-1.19	Pathogenic	0.22	Tolerated	3.37	34	1	2	2.3	-32.06																10.1016/j.ajhg.2020.11.011
c.1802C>T	A601V (3D Viewer)	GAP	Uncertain		1				-10.447	Likely Pathogenic	0.853	Likely Pathogenic	Ambiguous	0.535	Likely Pathogenic	1.64	Ambiguous	0.1	0.35	Likely Benign	1.00	Ambiguous	0.81	Ambiguous	-3.98	Deleterious	1.000	Probably Damaging	0.989	Probably Damaging	2.74	Benign	0.03	Affected	3.37	35	0	0	2.4	28.05	228.5	-45.5	0.0	0.0	0.4	0.5						X		Potentially Benign	The methyl side chain of Ala601, located on an α helix (res. Glu582-Met603), packs hydrophobically against other hydrophobic residues in the inter-helix space (e.g., Phe597, Leu598, Leu506, Phe608).In the variant simulations, Val601, which has similar size and physicochemical properties to alanine, resides in the inter-helix hydrophobic space in a similar manner to Ala601 in the WT, causing no apparent negative effect on the protein structure. However, the effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1091C>A	P364H (3D Viewer)	C2				6-33437996-C-A			-10.744	Likely Pathogenic	0.631	Likely Pathogenic	Likely Benign	0.407	Likely Benign	1.65	Ambiguous	0.9	0.25	Likely Benign	0.95	Ambiguous	0.77	Ambiguous	-6.96	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.55	Pathogenic	0.02	Affected	3.39	20	-2	0	-1.6	40.02
c.1753G>A	A585T (3D Viewer)	GAP				6-33440805-G-A	13	8.05e-6	-10.063	Likely Pathogenic	0.876	Likely Pathogenic	Ambiguous	0.465	Likely Benign	1.66	Ambiguous	0.2	1.97	Ambiguous	1.82	Ambiguous	0.23	Likely Benign	-1.73	Neutral	1.000	Probably Damaging	0.994	Probably Damaging	-1.30	Pathogenic	0.26	Tolerated	3.37	35	0	1	-2.5	30.03
c.1691A>G	E564G (3D Viewer)	GAP				6-33440743-A-G			-15.053	Likely Pathogenic	0.969	Likely Pathogenic	Likely Pathogenic	0.735	Likely Pathogenic	1.69	Ambiguous	0.1	2.55	Destabilizing	2.12	Destabilizing	0.80	Ambiguous	-6.83	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	-1.23	Pathogenic	0.04	Affected	3.37	35	-2	0	3.1	-72.06
c.1465C>T	L489F (3D Viewer)	GAP	Uncertain		2	6-33438497-C-T	1	6.20e-7	-12.066	Likely Pathogenic	0.965	Likely Pathogenic	Likely Pathogenic	0.724	Likely Pathogenic	1.72	Ambiguous	0.5	1.14	Ambiguous	1.43	Ambiguous	0.56	Ambiguous	-3.76	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	-1.51	Pathogenic	0.01	Affected	3.37	35	2	0	-1.0	34.02	246.4	-17.8	0.0	0.0	0.6	0.1						X		Potentially Benign	The iso-butyl side chain of Leu489, located in the α-helix (res. Leu489-Glu519) within an inter-helix space of four helices (res. Ala461-Phe476, res. Val441-Ser457, and res. Met414-Glu436), packs with hydrophobic residues (e.g., Cys432, Ala448, Lys444, Ala493, Val447, Met468) in the inter-helix space. In the variant simulations, the phenyl ring of the Phe489 side chain can also pack favorably in the hydrophobic region. However, due to the size difference, the aromatic side chain of Phe489 tends to reposition to escape the tight region to accommodate the larger side chain, stacking with Lys444. Although no apparent negative changes are observed during the variant simulation, the size difference between the swapped residues could affect the protein folding process.
c.1841A>C	Y614S (3D Viewer)	GAP				6-33440893-A-C	1	6.20e-7	-12.709	Likely Pathogenic	0.990	Likely Pathogenic	Likely Pathogenic	0.482	Likely Benign	1.74	Ambiguous	0.4	3.25	Destabilizing	2.50	Destabilizing	2.05	Destabilizing	-8.83	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.48	Benign	0.09	Tolerated	3.37	35	-2	-3	0.5	-76.10
c.1907T>G	F636C (3D Viewer)	GAP				6-33440959-T-G	3	1.86e-6	-13.287	Likely Pathogenic	0.972	Likely Pathogenic	Likely Pathogenic	0.612	Likely Pathogenic	1.74	Ambiguous	0.1	2.65	Destabilizing	2.20	Destabilizing	1.22	Destabilizing	-7.67	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	3.40	Benign	0.04	Affected	3.37	34	-2	-4	-0.3	-44.04
c.1260T>G	F420L (3D Viewer)	GAP	Uncertain		1				-8.432	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.146	Likely Benign	1.76	Ambiguous	0.0	1.41	Ambiguous	1.59	Ambiguous	1.04	Destabilizing	-5.39	Deleterious	0.009	Benign	0.005	Benign	4.22	Benign	0.39	Tolerated	3.37	29	2	0	1.0	-34.02	231.1	13.2	0.0	0.0	-0.1	0.0						X		Potentially Benign	In the WT, the phenyl ring of the Phe420 side chain, located on an α helix (res. Met414-Glu436), packs against hydrophobic residues in the interhelix area of the GAP domain (e.g., Leu689, Leu714, Leu717, Leu718). In the variant simulations, the iso-butyl side chain of Leu420 also packs into the hydrophobic inter-helix niche, but due to its smaller size, the resulting steric interactions are not as favorable as with phenylalanine. In short, the residue swap does not cause severe effects on the protein structure based on the variant simulations.
c.1646T>C	L549S (3D Viewer)	GAP				6-33438889-T-C	1	6.20e-7	-13.018	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.801	Likely Pathogenic	1.76	Ambiguous	0.4	1.03	Ambiguous	1.40	Ambiguous	1.01	Destabilizing	-4.85	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.14	Pathogenic	0.34	Tolerated	3.37	35	-2	-3	-4.6	-26.08
c.827C>G	P276R (3D Viewer)	C2				6-33437732-C-G	7	4.34e-6	-10.983	Likely Pathogenic	0.714	Likely Pathogenic	Likely Benign	0.498	Likely Benign	1.78	Ambiguous	0.2	1.02	Ambiguous	1.40	Ambiguous	0.78	Ambiguous	-4.52	Deleterious	0.994	Probably Damaging	0.892	Possibly Damaging	1.89	Pathogenic	0.01	Affected	3.38	19	-2	0	-2.9	59.07
c.1192C>G	P398A (3D Viewer)	C2				6-33438097-C-G	2	1.24e-6	-5.321	Likely Benign	0.184	Likely Benign	Likely Benign	0.290	Likely Benign	1.80	Ambiguous	0.2	1.15	Ambiguous	1.48	Ambiguous	0.92	Ambiguous	-5.17	Deleterious	0.008	Benign	0.005	Benign	5.55	Benign	0.12	Tolerated	3.40	16	-1	1	3.4	-26.04
c.1873C>G	L625V		Uncertain		1				-11.319	Likely Pathogenic	0.833	Likely Pathogenic	Ambiguous	0.480	Likely Benign	1.80	Ambiguous	0.7	1.69	Ambiguous	1.75	Ambiguous	1.42	Destabilizing	-2.96	Deleterious	0.998	Probably Damaging	0.992	Probably Damaging	3.07	Benign	0.01	Affected			2	1	0.4	-14.03
c.1240A>G	M414V		Uncertain		1				-8.003	Likely Pathogenic	0.541	Ambiguous	Likely Benign	0.261	Likely Benign	1.81	Ambiguous	0.4	1.73	Ambiguous	1.77	Ambiguous	0.95	Ambiguous	-2.95	Deleterious	0.999	Probably Damaging	0.987	Probably Damaging	3.43	Benign	0.24	Tolerated			2	1	2.3	-32.06
c.1487A>G	E496G (3D Viewer)	GAP	Uncertain		1				-13.529	Likely Pathogenic	0.850	Likely Pathogenic	Ambiguous	0.825	Likely Pathogenic	1.83	Ambiguous	0.1	1.76	Ambiguous	1.80	Ambiguous	0.92	Ambiguous	-6.16	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.45	Pathogenic	0.02	Affected	3.37	35	0	-2	3.1	-72.06	173.9	103.1	0.0	0.0	-0.7	0.0		X		X				Potentially Pathogenic	Glu496 is located in the α-helix (res. Leu489-Glu519), and its carboxylate group forms salt bridges with the neighbouring residues Lys492 and Arg499 in the WT simulations. Glu496 also forms a hydrogen bond with Ser449 on an opposing helix (res. Val441-Ser457). In the variant simulations, Gly496 cannot form these salt bridges, which could weaken the secondary structure. Additionally, the loss of the hydrogen bond with Ser449 on the opposite helix can weaken the tertiary structure assembly. Moreover, glycine is an α-helix breaker, and it is seen to weaken the integrity of the helix as the hydrogen bonding between the backbone atoms of Gly496 and Ala493 breaks down. Also, due to its location at the GAP-Ras interface, the interaction of Glu496 with Arg499 and Lys492 might play a role in complex association and stability, which cannot be fully addressed using the SynGAP solvent-only simulations.
c.1165T>C	S389P (3D Viewer)	C2				6-33438070-T-C			-5.286	Likely Benign	0.130	Likely Benign	Likely Benign	0.460	Likely Benign	1.85	Ambiguous	2.0	-0.99	Ambiguous	0.43	Likely Benign	0.16	Likely Benign	-0.44	Neutral	0.676	Possibly Damaging	0.693	Possibly Damaging	5.05	Benign	0.01	Affected	4.32	8	-1	1	-0.8	10.04
c.719A>G	D240G	PH	Uncertain		1				-12.825	Likely Pathogenic	0.951	Likely Pathogenic	Ambiguous	0.912	Likely Pathogenic	1.85	Ambiguous	0.1	2.72	Destabilizing	2.29	Destabilizing	0.24	Likely Benign	-6.19	Deleterious	0.993	Probably Damaging	0.984	Probably Damaging	5.79	Benign	0.01	Affected			1	-1	3.1	-58.04
c.895C>T	R299C (3D Viewer)	C2	Conflicting		2	6-33437800-C-T	3	1.86e-6	-6.326	Likely Benign	0.572	Likely Pathogenic	Likely Benign	0.344	Likely Benign	1.85	Ambiguous	0.4	0.61	Ambiguous	1.23	Ambiguous	0.76	Ambiguous	-3.54	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.65	Pathogenic	0.06	Tolerated	3.39	19	-4	-3	7.0	-53.05	210.7	91.3	0.1	0.0	0.0	0.2	X	X						Potentially Pathogenic	The guanidinium group of Arg299, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Met289-Pro298, res. Thr305-Asn315), forms hydrogen bonds that stabilize the tight turn. In the WT simulations, the Arg299 side chain hydrogen bonds with the loop backbone carbonyl groups (e.g., Ser302, Thr305, Leu274, Gly303), the hydroxyl group of Ser300, and even forms a salt bridge with the carboxylate group of Asp304.In the variant simulations, the thiol group of the Cys299 side chain is unable to form any of these well-coordinated or strong interactions, which could affect the initial formation of the secondary hairpin loop during folding. β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Moreover, the positively charged Arg299 side chain faces the polar head group region of the inner leaflet membrane and could directly anchor the C2 domain to the membrane. In short, the residue swap could negatively affect both protein folding and the stability of the SynGAP-membrane association.
c.823C>G	P275A (3D Viewer)	C2				6-33437728-C-G	1	6.20e-7	-6.137	Likely Benign	0.133	Likely Benign	Likely Benign	0.410	Likely Benign	1.87	Ambiguous	0.2	1.11	Ambiguous	1.49	Ambiguous	0.50	Likely Benign	-4.95	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.79	Pathogenic	0.32	Tolerated	3.38	19	-1	1	3.4	-26.04
c.908G>A	G303E (3D Viewer)	C2				6-33437813-G-A	3	1.86e-6	-9.339	Likely Pathogenic	0.549	Ambiguous	Likely Benign	0.063	Likely Benign	1.87	Ambiguous	0.5	0.37	Likely Benign	1.12	Ambiguous	0.89	Ambiguous	-1.56	Neutral	0.001	Benign	0.005	Benign	4.04	Benign	0.05	Affected	3.55	18	-2	0	-3.1	72.06
c.930G>C	E310D (3D Viewer)	C2	Likely Pathogenic		1				-11.218	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.666	Likely Pathogenic	1.87	Ambiguous	0.5	2.39	Destabilizing	2.13	Destabilizing	1.04	Destabilizing	-2.76	Deleterious	0.997	Probably Damaging	0.992	Probably Damaging	1.19	Pathogenic	0.02	Affected	3.38	19	3	2	0.0	-14.03	232.6	27.2	0.1	0.0	0.1	0.1						X		Potentially Benign	The carboxylate group of Glu310, located in an anti-parallel β sheet strand (res. Thr305-Asn315), is ideally positioned to interact with the hydroxyl and backbone amide groups of Thr295 on a twisted anti-parallel β strand. Because the carboxylate group can also interact with the GAP domain residues (e.g., Gln612, Tyr614), Glu310 potentially plays a key role in maintaining the tertiary assembly between the C2 and GAP domains. In the variant simulations, the carboxylate group of Asp310 can form the same interactions as glutamate; however, due to its one hydrocarbon shorter length, the connections are less stable or less optimal.
c.1289T>C	M430T (3D Viewer)	GAP				6-33438194-T-C	1	6.19e-7	-3.430	Likely Benign	0.107	Likely Benign	Likely Benign	0.103	Likely Benign	1.89	Ambiguous	0.1	0.01	Likely Benign	0.95	Ambiguous	0.43	Likely Benign	-1.48	Neutral	0.016	Benign	0.010	Benign	3.48	Benign	0.40	Tolerated	3.37	29	-1	-1	-2.6	-30.09
c.1792C>G	L598V (3D Viewer)	GAP	Uncertain		1				-10.002	Likely Pathogenic	0.578	Likely Pathogenic	Likely Benign	0.221	Likely Benign	1.89	Ambiguous	0.1	1.58	Ambiguous	1.74	Ambiguous	1.01	Destabilizing	-2.92	Deleterious	0.944	Possibly Damaging	0.786	Possibly Damaging	3.21	Benign	0.02	Affected	3.37	35	2	1	0.4	-14.03	218.4	29.6	0.0	0.0	0.8	0.0						X		Potentially Benign	The iso-butyl side chain of Leu598, located on an α helix (res. Glu582-Met603), packs hydrophobically with other hydrophobic residues in the inter-helix space (e.g., Ile602, Phe594, Ile510).In the variant simulations, Val598, which has similar size and physicochemical properties to leucine, resides in the inter-helix hydrophobic space in a similar manner to Leu598 in the WT. This causes no negative effects on the protein structure.
c.1703T>C	V568A (3D Viewer)	GAP				6-33440755-T-C	2	1.25e-6	-10.929	Likely Pathogenic	0.946	Likely Pathogenic	Ambiguous	0.834	Likely Pathogenic	1.90	Ambiguous	0.1	1.77	Ambiguous	1.84	Ambiguous	2.16	Destabilizing	-3.82	Deleterious	0.999	Probably Damaging	0.990	Probably Damaging	-1.38	Pathogenic	0.06	Tolerated	3.37	35	0	0	-2.4	-28.05
c.790C>A	L264I (3D Viewer)	C2				6-33437695-C-A	1	6.20e-7	-10.945	Likely Pathogenic	0.638	Likely Pathogenic	Likely Benign	0.418	Likely Benign	1.90	Ambiguous	0.5	0.84	Ambiguous	1.37	Ambiguous	0.95	Ambiguous	-1.84	Neutral	0.999	Probably Damaging	0.994	Probably Damaging	0.66	Pathogenic	0.02	Affected	3.38	18	2	2	0.7	0.00
c.1045C>T	P349S (3D Viewer)	C2	Uncertain		1				-7.654	In-Between	0.217	Likely Benign	Likely Benign	0.277	Likely Benign	1.92	Ambiguous	0.1	2.28	Destabilizing	2.10	Destabilizing	0.87	Ambiguous	-6.13	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	1.66	Pathogenic	0.06	Tolerated	3.37	25	1	-1	0.8	-10.04	194.9	-18.1	-0.1	0.0	0.2	0.1	X						X	Potentially Pathogenic	The cyclic pyrrolidine side chain of Pro349, located at the end of an anti-parallel β sheet strand (res. Gly341-Pro349), allows the strand to end and make a tight turn before a short α helical section within a loop connecting to another β strand (res. Thr359-Pro364). In the variant simulations, the hydroxyl group of Ser349 forms a hydrogen bond with the backbone amide group of Ala351 in the short helical section. Conversely, the backbone amide group of Ser349 (absent in proline) does not form any intra-protein hydrogen bonds. However, the β strand end connects to the α helical section in a more stable and consistent manner compared to the WT. Although the residue swap does not cause major adverse effects on the protein structure in the simulations, it is possible that the tight turn at the β strand end could not be created during folding without the presence of proline.
c.1150G>A	G384S (3D Viewer)	C2	Uncertain		1	6-33438055-G-A	1	6.22e-7	-5.243	Likely Benign	0.090	Likely Benign	Likely Benign	0.315	Likely Benign	1.92	Ambiguous	0.2	1.66	Ambiguous	1.79	Ambiguous	0.19	Likely Benign	-0.67	Neutral	0.980	Probably Damaging	0.968	Probably Damaging	1.33	Pathogenic	0.04	Affected	4.32	2	1	0	-0.4	30.03	202.4	-49.8	0.5	1.0	-0.2	0.0								Uncertain	Gly384 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and so they are rich in glycines, prolines, and, to a lesser extent, small hydrophilic residues to ensure maximum flexibility. Thus, the variant’s Ser384 is potentially tolerated in the Ω loop, although the hydroxyl group of Ser384 forms various hydrogen bonds with several other loop residues in the variant simulations. However, since the effects on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1531G>A	G511R (3D Viewer)	GAP	Likely Pathogenic		1				-11.327	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.416	Likely Benign	1.94	Ambiguous	0.3	1.32	Ambiguous	1.63	Ambiguous	0.94	Ambiguous	-7.72	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.26	Benign	0.06	Tolerated	3.37	35	-3	-2	-4.1	99.14	279.4	-159.9	0.0	0.0	0.7	0.1			X				X	Potentially Pathogenic	Gly511 is located in an α-helix (res. Gly502-Tyr518), facing hydrophobic residues in an inter-helix space (e.g., Leu610, Ile514) in the WT simulations. In contrast, in the variant simulations, the bulkier and positively charged guanidinium side chain of Arg511 forms a salt bridge with the carboxylate group of Glu217 or hydrogen bonds with the backbone carbonyl group of Leu610. Although the residue swap introduces a third positively charged residue in close vicinity (Arg511, Lys507, Arg515), the protein structure seems to remain stable in the variant simulations. Importantly, according to ClinVar, the residue swap alters the last nucleotide of an exon and is predicted to destroy the splice donor site, resulting in aberrant splicing and pathogenic status.	10.1016/j.ajhg.2020.11.011
c.1531G>C	G511R (3D Viewer)	GAP	Pathogenic		1				-11.327	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.415	Likely Benign	1.94	Ambiguous	0.3	1.32	Ambiguous	1.63	Ambiguous	0.94	Ambiguous	-7.72	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.26	Benign	0.06	Tolerated	3.37	35	-3	-2	-4.1	99.14	279.4	-159.9	0.0	0.0	0.7	0.1			X				X	Potentially Pathogenic	Gly511 is located in an α-helix (res. Gly502-Tyr518), facing hydrophobic residues in an inter-helix space (e.g., Leu610, Ile514) in the WT simulations. In contrast, in the variant simulations, the bulkier and positively charged guanidinium side chain of Arg511 forms a salt bridge with the carboxylate group of Glu217 or hydrogen bonds with the backbone carbonyl group of Leu610. Although the residue swap introduces a third positively charged residue in close vicinity (Arg511, Lys507, Arg515), the protein structure seems to remain stable in the variant simulations. Importantly, according to ClinVar, the residue swap alters the last nucleotide of an exon and is predicted to destroy the splice donor site, resulting in aberrant splicing and pathogenic status.	10.1016/j.ajhg.2020.11.011
c.1160G>C	G387A (3D Viewer)	C2				6-33438065-G-C	3	1.87e-6	-6.313	Likely Benign	0.104	Likely Benign	Likely Benign	0.300	Likely Benign	1.95	Ambiguous	0.1	1.68	Ambiguous	1.82	Ambiguous	-0.02	Likely Benign	-0.29	Neutral	0.007	Benign	0.010	Benign	1.33	Pathogenic	0.06	Tolerated	4.32	3	0	1	2.2	14.03
c.775C>T	R259W (3D Viewer)	C2	Uncertain		1				-12.186	Likely Pathogenic	0.985	Likely Pathogenic	Likely Pathogenic	0.691	Likely Pathogenic	1.95	Ambiguous	0.8	0.51	Ambiguous	1.23	Ambiguous	0.51	Ambiguous	-7.35	Deleterious	1.000	Probably Damaging	0.993	Probably Damaging	5.76	Benign	0.00	Affected	3.39	15	2	-3	3.6	30.03	254.0	40.0	0.2	0.2	0.2	0.4	X	X					X	Potentially Pathogenic	The guanidinium group of Arg259, located at the beginning of an anti-parallel β sheet strand (res. Arg259-Arg272), forms salt bridges with the carboxylate groups of Asp684 at the end of an α helix (res. Ile683-Gln702, GAP domain) and Asp261 on the same β strand. The Arg259 side chain also frequently forms hydrogen bonds with the backbone carbonyl groups of Ser257, Asn256, and Asp255. In the variant simulations, the indole ring of the Trp259 side chain cannot form salt bridges or maintain hydrogen bonding with the carboxylate group of Asp684 or other nearby residues. Notably, the amino group of the Lys254 side chain maintains a salt bridge with Asp684 and Glu244 throughout the variant simulations, while it forms a cation-π bond with the indole ring of Trp259 in the variant. This salt bridge is not maintained in the WT simulations. Additionally, the partially or loosely α helical conformation of a lysine-containing loop (res. Lys251-Ser257), which extends to a nearby α helix (res. Met414-Asn426), could be stabilized due to the residue swap. Moreover, the bulky size of the Trp259 side chain requires nearby residues to adjust their positioning to accommodate the introduced residue, weakening the tertiary structure assembly between the C2, PH, and GAP domains. The residue swap potentially causes more severe effects during protein folding or for the SynGAP-membrane interaction than the solvent-only simulations imply.
c.716G>C	R239T (3D Viewer)	PH				6-33435567-G-C	1	6.19e-7	-14.792	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.869	Likely Pathogenic	1.96	Ambiguous	0.3	2.44	Destabilizing	2.20	Destabilizing	1.21	Destabilizing	-5.35	Deleterious	0.259	Benign	0.064	Benign	5.66	Benign	0.01	Affected	3.40	14	-1	-1	3.8	-55.08
c.806T>C	I269T (3D Viewer)	C2				6-33437711-T-C	2	1.24e-6	-9.376	Likely Pathogenic	0.887	Likely Pathogenic	Ambiguous	0.727	Likely Pathogenic	1.97	Ambiguous	0.1	2.10	Destabilizing	2.04	Destabilizing	1.38	Destabilizing	-3.70	Deleterious	0.997	Probably Damaging	0.994	Probably Damaging	1.72	Pathogenic	0.09	Tolerated	3.38	19	-1	0	-5.2	-12.05
c.928G>A	E310K (3D Viewer)	C2	Conflicting		4				-14.601	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.764	Likely Pathogenic	1.97	Ambiguous	1.2	3.66	Destabilizing	2.82	Destabilizing	1.02	Destabilizing	-3.68	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	1.19	Pathogenic	0.01	Affected	3.38	19	0	1	-0.4	-0.94	213.4	58.0	0.1	0.0	0.2	0.1		X						Potentially Pathogenic	The carboxylate group of Glu310, located in an anti-parallel β sheet strand (res. Thr305-Asn315), is ideally positioned to interact with the side chain hydroxyl and backbone amide groups of Thr295 on a twisted anti-parallel β strand (res. Met289-Arg299). Because the carboxylate group can also interact with the GAP domain residues (e.g., Gln612, Tyr614), Glu310 plays a key role in maintaining the tertiary assembly between the C2 and GAP domains. In the variant simulations, the amino group of the Lys310 side chain hydrogen bonds with the GAP domain residues and forms a salt bridge with Glu613. Although no apparent negative effects are seen due to the residue swap, it is possible that the loss of hydrogen bonding with the hydroxyl group of the Thr295 side chain causes problems during folding, potentially compromising the twisting of the β sheet.
c.1832T>C	M611T (3D Viewer)	GAP				6-33440884-T-C	1	6.19e-7	-5.696	Likely Benign	0.101	Likely Benign	Likely Benign	0.240	Likely Benign	1.98	Ambiguous	0.2	0.94	Ambiguous	1.46	Ambiguous	0.87	Ambiguous	-2.40	Neutral	0.034	Benign	0.038	Benign	-1.19	Pathogenic	0.29	Tolerated	3.37	35	-1	-1	-2.6	-30.09
c.827C>A	P276H (3D Viewer)	C2				6-33437732-C-A	1	6.20e-7	-10.469	Likely Pathogenic	0.575	Likely Pathogenic	Likely Benign	0.534	Likely Pathogenic	1.98	Ambiguous	0.1	1.09	Ambiguous	1.54	Ambiguous	0.85	Ambiguous	-4.80	Deleterious	1.000	Probably Damaging	0.961	Probably Damaging	1.84	Pathogenic	0.00	Affected	3.38	19	-2	0	-1.6	40.02
c.835C>T	R279W (3D Viewer)	C2	Uncertain		1				-11.417	Likely Pathogenic	0.942	Likely Pathogenic	Ambiguous	0.485	Likely Benign	2.00	Destabilizing	0.8	1.47	Ambiguous	1.74	Ambiguous	0.80	Ambiguous	-6.29	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.88	Pathogenic	0.00	Affected	3.39	18	2	-3	3.6	30.03	270.0	38.3	0.1	0.0	0.3	0.0								Uncertain	The guanidinium group of Arg279, located at the beginning of an anti-parallel β sheet strand (res. Arg279-Leu286), can form hydrogen bond with the backbone carbonyl groups of nearby loop residues (e.g., Ser296, Ser331, and As332) and form salt bridges with the carboxylate groups of Asp330 and Asp332. In the WT simulations, Arg279 sporadically forms a salt bridge even with the carboxylate group of Glu613, loosely connecting the C2 domain and GAP domain. Meanwhile, the indole ring of the Trp279 side chain is unable to hydrogen bond with the loop residues in the variant simulations. The lack of hydrogen bond or salt bridge formation with the loop residues could be significant, as Arg279 and the loops face the polar head group region of the membrane. Thus, although Trp279 could interact with the membrane surface as a “lipid anchor,” any changes to the wider loop dynamics could still adversely affect the formation of a stable SynGAP-membrane association. However, no definite conclusions on the effect of the residue swap on the SynGAP-membrane association can be drawn from solvent-only simulations.
c.1802C>G	A601G (3D Viewer)	GAP				6-33440854-C-G	1	6.19e-7	-11.772	Likely Pathogenic	0.543	Ambiguous	Likely Benign	0.511	Likely Pathogenic	2.03	Destabilizing	0.0	2.31	Destabilizing	2.17	Destabilizing	0.94	Ambiguous	-3.98	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	2.55	Benign	0.01	Affected	3.37	35	0	1	-2.2	-14.03
c.1427T>G	F476C (3D Viewer)	GAP				6-33438459-T-G			-9.270	Likely Pathogenic	0.745	Likely Pathogenic	Likely Benign	0.280	Likely Benign	2.05	Destabilizing	0.1	2.62	Destabilizing	2.34	Destabilizing	-0.30	Likely Benign	2.69	Neutral	1.000	Probably Damaging	0.999	Probably Damaging	3.46	Benign	0.83	Tolerated	3.40	22	-2	-4	-0.3	-44.04
c.1151G>A	G384D (3D Viewer)	C2				6-33438056-G-A			-9.142	Likely Pathogenic	0.610	Likely Pathogenic	Likely Benign	0.439	Likely Benign	2.06	Destabilizing	0.5	2.15	Destabilizing	2.11	Destabilizing	0.53	Ambiguous	-0.93	Neutral	0.994	Probably Damaging	0.986	Probably Damaging	1.32	Pathogenic	0.04	Affected	4.32	2	-1	1	-3.1	58.04
c.1784T>C	L595P (3D Viewer)	GAP	Uncertain		1				-11.856	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.747	Likely Pathogenic	2.09	Destabilizing	0.8	5.88	Destabilizing	3.99	Destabilizing	1.78	Destabilizing	-6.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.72	Benign	0.00	Affected	3.37	35	-3	-3	-5.4	-16.04
c.736C>G	L246V (3D Viewer)	PH				6-33435587-C-G	1	6.20e-7	-12.092	Likely Pathogenic	0.935	Likely Pathogenic	Ambiguous	0.736	Likely Pathogenic	2.09	Destabilizing	0.1	1.52	Ambiguous	1.81	Ambiguous	1.13	Destabilizing	-2.60	Deleterious	0.930	Possibly Damaging	0.504	Possibly Damaging	4.71	Benign	0.01	Affected	3.41	14	1	2	0.4	-14.03
c.1304T>G	L435W (3D Viewer)	GAP	Uncertain		1				-14.889	Likely Pathogenic	0.992	Likely Pathogenic	Likely Pathogenic	0.572	Likely Pathogenic	2.11	Destabilizing	0.1	0.69	Ambiguous	1.40	Ambiguous	1.66	Destabilizing	-5.63	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	3.15	Benign	0.00	Affected	3.37	29	-2	-2	-4.7	73.05	242.2	-25.2	0.0	0.0	0.3	0.1							X	Potentially Pathogenic	The iso-butyl side chain of Leu435, located in an α helix (res. Met414-Glu436), packs against other hydrophobic residues in an interhelix space (e.g., Val699, Val447, Leu489, Leu439) in the WT simulations. In the variant simulations, the indole ring of Trp435 fits into the same niche despite its considerably bulkier size. Additionally, the side chain forms an H-bond with the backbone carbonyl of Leu696 in an α helix (res. Asp684-Gln702). Although no apparent negative changes are observed during the variant simulation, the size difference between the swapped residues could affect the protein folding process.
c.823C>T	P275S (3D Viewer)	C2				6-33437728-C-T	1	6.20e-7	-7.886	In-Between	0.312	Likely Benign	Likely Benign	0.388	Likely Benign	2.11	Destabilizing	0.3	1.28	Ambiguous	1.70	Ambiguous	0.77	Ambiguous	-5.24	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.78	Pathogenic	0.03	Affected	3.38	19	-1	1	0.8	-10.04
c.1088A>G	Y363C (3D Viewer)	C2				6-33437993-A-G	1	7.13e-7	-9.059	Likely Pathogenic	0.721	Likely Pathogenic	Likely Benign	0.414	Likely Benign	2.21	Destabilizing	0.1	3.96	Destabilizing	3.09	Destabilizing	2.05	Destabilizing	-8.07	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	1.54	Pathogenic	0.00	Affected	3.39	24	-2	0	3.8	-60.04
c.952C>T	P318S (3D Viewer)	C2				6-33437857-C-T	1	6.19e-7	-9.954	Likely Pathogenic	0.956	Likely Pathogenic	Likely Pathogenic	0.626	Likely Pathogenic	2.22	Destabilizing	0.1	1.71	Ambiguous	1.97	Ambiguous	1.00	Destabilizing	-7.05	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.87	Pathogenic	0.03	Affected	3.38	23	-1	1	0.8	-10.04
c.1828C>G	L610V (3D Viewer)	GAP				6-33440880-C-G	3	1.86e-6	-11.304	Likely Pathogenic	0.474	Ambiguous	Likely Benign	0.740	Likely Pathogenic	2.24	Destabilizing	0.3	0.76	Ambiguous	1.50	Ambiguous	1.21	Destabilizing	-2.86	Deleterious	0.985	Probably Damaging	0.992	Probably Damaging	-1.46	Pathogenic	0.01	Affected	3.37	35	1	2	0.4	-14.03
c.2041G>C	G681R (3D Viewer)	GAP				6-33441300-G-C	1	6.20e-7	-12.170	Likely Pathogenic	0.992	Likely Pathogenic	Likely Pathogenic	0.556	Likely Pathogenic	2.25	Destabilizing	1.7	5.46	Destabilizing	3.86	Destabilizing	0.99	Ambiguous	-7.98	Deleterious	0.999	Probably Damaging	0.928	Probably Damaging	3.42	Benign	0.00	Affected	3.43	14	-2	-3	-4.1	99.14
c.1718G>A	R573Q (3D Viewer)	GAP	Likely Pathogenic		1				-9.900	Likely Pathogenic	0.923	Likely Pathogenic	Ambiguous	0.733	Likely Pathogenic	2.28	Destabilizing	0.8	1.94	Ambiguous	2.11	Destabilizing	1.08	Destabilizing	-3.16	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	-1.31	Pathogenic	0.12	Tolerated	3.37	35	1	1	1.0	-28.06	230.1	49.9	0.0	0.0	-0.6	0.0	X	X						Potentially Pathogenic	The guanidinium group of Arg573, located in an α-helix (res. Arg563-Glu578), forms a salt bridge with the carboxylate groups of Glu582 and/or Asp586 from a nearby α-helix (res. Glu582-Met603) in the WT simulations. Additionally, the Arg573 side chain stacks planarly with the aromatic phenol ring of Tyr665 and hydrogen bonds with the hydroxyl group of Ser668 from another α-helix (res. Ser641-Ser668). In the variant simulations, although the carboxamide group of the Gln573 side chain can hydrogen bond with the carboxylate group of Glu582 or the hydroxyl group of Ser668, these interactions are not as coordinated, stable, or strong as those of the positively charged Arg573. Consequently, the integrity of the opposing α-helix end (res. Glu582-Met603) is weakened. Overall, the residue swap has the potential to substantially affect the tertiary structure assembly during the protein folding process.
c.1126G>A	G376S (3D Viewer)	C2				6-33438031-G-A	1	6.21e-7	-4.913	Likely Benign	0.087	Likely Benign	Likely Benign	0.471	Likely Benign	2.30	Destabilizing	0.5	-0.45	Likely Benign	0.93	Ambiguous	0.32	Likely Benign	-0.73	Neutral	1.000	Probably Damaging	0.998	Probably Damaging	1.33	Pathogenic	0.22	Tolerated	4.32	12	0	1	-0.4	30.03
c.679G>C	G227R (3D Viewer)	PH				6-33435530-G-C	1	6.20e-7	-9.776	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.765	Likely Pathogenic	2.31	Destabilizing	0.3	5.29	Destabilizing	3.80	Destabilizing	0.90	Ambiguous	-6.49	Deleterious	0.020	Benign	0.018	Benign	6.02	Benign	0.01	Affected	3.43	12	-2	-3	-4.1	99.14
c.1897C>G	L633V (3D Viewer)	GAP				6-33440949-C-G	1	6.20e-7	-9.992	Likely Pathogenic	0.759	Likely Pathogenic	Likely Benign	0.327	Likely Benign	2.32	Destabilizing	0.2	1.71	Ambiguous	2.02	Destabilizing	1.32	Destabilizing	-2.99	Deleterious	0.996	Probably Damaging	0.992	Probably Damaging	2.86	Benign	0.03	Affected	3.37	34	1	2	0.4	-14.03
c.1540A>T	I514F (3D Viewer)	GAP	Uncertain		1				-13.383	Likely Pathogenic	0.962	Likely Pathogenic	Likely Pathogenic	0.601	Likely Pathogenic	2.35	Destabilizing	0.3	3.74	Destabilizing	3.05	Destabilizing	0.93	Ambiguous	-3.98	Deleterious	0.997	Probably Damaging	0.993	Probably Damaging	2.89	Benign	0.00	Affected	3.37	35	0	1	-1.7	34.02
c.2086C>G	L696V (3D Viewer)	GAP	Uncertain		1				-11.909	Likely Pathogenic	0.745	Likely Pathogenic	Likely Benign	0.351	Likely Benign	2.35	Destabilizing	0.1	1.85	Ambiguous	2.10	Destabilizing	1.46	Destabilizing	-2.79	Deleterious	0.992	Probably Damaging	0.970	Probably Damaging	3.16	Benign	0.00	Affected	3.46	13	1	2	0.4	-14.03
c.623C>T	P208L (3D Viewer)	PH				6-33435265-C-T	1	6.20e-7	-10.013	Likely Pathogenic	0.889	Likely Pathogenic	Ambiguous	0.466	Likely Benign	2.35	Destabilizing	0.5	0.04	Likely Benign	1.20	Ambiguous	0.67	Ambiguous	-8.49	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	3.75	Benign	0.01	Affected	3.44	12	-3	-3	5.4	16.04
c.1159G>A	G387S (3D Viewer)	C2				6-33438064-G-A			-4.674	Likely Benign	0.089	Likely Benign	Likely Benign	0.359	Likely Benign	2.37	Destabilizing	0.5	1.94	Ambiguous	2.16	Destabilizing	0.12	Likely Benign	-0.12	Neutral	0.000	Benign	0.002	Benign	1.33	Pathogenic	0.13	Tolerated	4.32	3	0	1	-0.4	30.03
c.1717C>T	R573W (3D Viewer)	GAP	Conflicting		8				-14.078	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.758	Likely Pathogenic	2.37	Destabilizing	0.7	0.57	Ambiguous	1.47	Ambiguous	0.88	Ambiguous	-6.94	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	-1.48	Pathogenic	0.00	Affected	3.37	35	2	-3	3.6	30.03	257.6	39.0	0.1	0.0	0.2	0.0	X	X						Potentially Pathogenic	The guanidinium group of Arg573, located in an α-helix (res. Arg563-Glu578), forms a salt bridge with the carboxylate groups of Glu582 and/or Asp586 from a nearby α-helix (res. Glu582-Met603) in the WT simulations. Additionally, the Arg573 side chain stacks planarly with the aromatic phenol ring of Tyr665 and hydrogen bonds with the hydroxyl group of Ser668 from another α-helix (res. Ser641-Ser668). In the variant simulations, the indole ring of the Trp573 side chain is unable to maintain the same level of coordination as the positively charged Arg573 side chain. Indeed, Trp573 is seen hydrogen bonding only briefly with the carboxylate group of Glu582. Consequently, the integrity of the opposing α-helix end (res. Glu582-Met603) is weakened. Overall, the residue swap has the potential to substantially affect the tertiary structure assembly during the protein folding process.
c.929A>G	E310G (3D Viewer)	C2	Pathogenic		1				-14.132	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.848	Likely Pathogenic	2.38	Destabilizing	0.7	3.56	Destabilizing	2.97	Destabilizing	0.36	Likely Benign	-6.43	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	1.12	Pathogenic	0.00	Affected	3.38	19	-2	0	3.1	-72.06
c.1502T>C	I501T (3D Viewer)	GAP	Uncertain		1				-5.996	Likely Benign	0.252	Likely Benign	Likely Benign	0.362	Likely Benign	2.40	Destabilizing	0.1	1.81	Ambiguous	2.11	Destabilizing	1.57	Destabilizing	-3.48	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.44	Benign	0.16	Tolerated	3.37	35	0	-1	-5.2	-12.05	214.5	26.9	0.0	0.0	0.5	0.0							X	Potentially Pathogenic	Ile501 is located near a hinge in the middle of an α-helix (res. Leu489-Glu519). The sec-butyl side chain of Ile501 is hydrophobically packed with other residues in the inter-helix space (e.g., Leu500, Tyr497, Phe679) in the WT simulations. In the variant simulations, the hydroxyl group of Thr501 forms a hydrogen bond with the backbone atoms of Tyr497 on the same α-helix, which may weaken the α-helix integrity. Additionally, the polar hydroxyl group of Thr501 is not suitable for the hydrophobic inter-helix space, and thus, the residue swap could affect protein folding. However, Ile501 is followed by Gly502, which facilitates a hinge in the middle of the α-helix, making further weakening caused by Thr501 unlikely to be harmful to the α-helix integrity.
c.1947G>C	M649I (3D Viewer)	GAP	Uncertain		1				-9.361	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.449	Likely Benign	2.42	Destabilizing	0.2	1.96	Ambiguous	2.19	Destabilizing	1.01	Destabilizing	-3.99	Deleterious	0.672	Possibly Damaging	0.093	Benign	3.40	Benign	0.02	Affected	3.38	27	2	1	2.6	-18.03	243.7	21.5	0.0	0.1	0.0	0.1							X	Potentially Benign	The thioether side chain of Met649, located on an α helix (res. Ser641-Glu666), bridges Phe652, Phe648, and Phe639 in an inter-helix hydrophobic cavity in the WT simulations. In the variant simulations, the sec-butyl side chain of Ile649 maintains hydrophobic interactions with nearby residues, with no significant effects on the protein structure.However, methionine is known as a bridging motif for aromatic residues, and these Met-aromatic interactions are lost in the variant. Indeed, in the second variant simulation,the bridging of Phe652, Phe648 and Phe639 is completely lost. In reality, the effect could be more severe on the structure during the protein folding.
c.823C>A	P275T (3D Viewer)	C2				6-33437728-C-A	3	1.86e-6	-8.708	Likely Pathogenic	0.309	Likely Benign	Likely Benign	0.425	Likely Benign	2.44	Destabilizing	0.3	1.15	Ambiguous	1.80	Ambiguous	0.69	Ambiguous	-5.38	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.75	Pathogenic	0.01	Affected	3.38	19	-1	0	0.9	3.99
c.1393C>G	L465V (3D Viewer)	GAP	Uncertain		1				-9.893	Likely Pathogenic	0.838	Likely Pathogenic	Ambiguous	0.276	Likely Benign	2.46	Destabilizing	0.1	2.66	Destabilizing	2.56	Destabilizing	1.21	Destabilizing	-2.98	Deleterious	0.996	Probably Damaging	0.992	Probably Damaging	2.44	Pathogenic	0.10	Tolerated	3.37	34	2	1	0.4	-14.03	204.3	30.9	0.0	0.0	-0.4	0.6						X		Potentially Benign	The iso-butyl side chain of Leu465, located in the middle of an α helix (res. Ala461–Phe476), packs with hydrophobic residues (e.g., Phe464, Met468, Tyr497, Ile494) in an inter-helix space formed with two other α helices (res. Ala461–Phe476 and res. Thr488-Gly502). In the variant simulations, the iso-propyl side chain of Val465 is equally sized and similarly hydrophobic as the original side chain of Leu465. Hence, the mutation does not exert any negative effects on the protein structure based on the variant simulations.
c.1621G>C	A541P (3D Viewer)	GAP	Uncertain		1				-14.733	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.594	Likely Pathogenic	2.47	Destabilizing	0.3	7.26	Destabilizing	4.87	Destabilizing	0.86	Ambiguous	-3.16	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	-1.34	Pathogenic	0.07	Tolerated	3.37	35	1	-1	-3.4	26.04	170.4	-11.2	0.1	0.0	0.1	0.0	X							Potentially Pathogenic	Ala541 is located on the outer surface of an α-helix (res. Ala533-Val560). The methyl group of Ala541 is on the surface and does not form any interactions. Proline lacks a free backbone amide group, and thus, Pro541 is unable to form a hydrogen bond with the carbonyl group of Ala537 in the variant simulations. Consequently, Pro541 disrupts the continuity of the secondary structure element, causing the α-helix to bend slightly in the variant simulations.
c.1025A>G	Y342C (3D Viewer)	C2	Conflicting		2	6-33437930-A-G	21	1.30e-5	-7.596	In-Between	0.682	Likely Pathogenic	Likely Benign	0.404	Likely Benign	2.48	Destabilizing	0.1	2.73	Destabilizing	2.61	Destabilizing	0.92	Ambiguous	-6.67	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.72	Pathogenic	0.02	Affected	3.37	25	0	-2	3.8	-60.04	242.4	62.8	0.1	0.0	-0.1	0.2								Potentially Pathogenic	The phenol ring of Tyr342, located at the end of an anti-parallel β sheet strand (res. Gly341-Pro349), faces outward in the C2 domain. This phenol ring contributes to a triple tyrosine stack (Tyr342, Tyr328, and Tyr281) that links together three anti-parallel β sheet strands. Additionally, it shields Gly344 from the solvent, reducing its exposure and providing stability for the β-sandwich. This motif also contributes to a twist formation in the β sheet.In the variant simulations, the Cys342 side chain cannot participate in the stack formation. Instead, its thiol group forms a hydrogen bond with the backbone carbonyl group of Leu327. Although these changes in surface interactions could weaken the characteristic twist that strengthens the β sheet fold, no major structural effects are observed in the variant simulations. The residue swap could also affect the SynGAP-membrane association; however, this phenomenon cannot be addressed using solvent-only simulations. Notably, the thiol group of cysteine is not a particularly strong hydrogen-bonding partner, which could mitigate the negative effects of the residue swap.
c.1652T>A	L551Q (3D Viewer)	GAP				6-33438895-T-A	1	6.20e-7	-13.632	Likely Pathogenic	0.990	Likely Pathogenic	Likely Pathogenic	0.936	Likely Pathogenic	2.48	Destabilizing	0.1	2.19	Destabilizing	2.34	Destabilizing	2.37	Destabilizing	-3.68	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.60	Pathogenic	0.01	Affected	3.37	35	-2	-2	-7.3	14.97
c.1466T>C	L489P (3D Viewer)	GAP	Conflicting		2				-13.520	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.939	Likely Pathogenic	2.50	Destabilizing	0.1	4.69	Destabilizing	3.60	Destabilizing	1.73	Destabilizing	-6.74	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.56	Pathogenic	0.00	Affected	3.37	35	-3	-3	-5.4	-16.04	209.9	61.9	0.1	0.0	0.6	0.1		X						Potentially Pathogenic	The iso-butyl side chain of Leu489, located in the α-helix (res. Leu489-Glu519) within an inter-helix space of four helices (res. Ala461-Phe476, res. Val441-Ser457, and res. Met414-Glu436), packs with hydrophobic residues (e.g., Cys432, Ala448, Lys444, Ala493, Val447, Met468). In the variant simulations, Pro489 is located near the beginning of the α-helix, so the residue swap with Leu489 does not affect the continuity of the secondary structure element. However, the side chain of proline is not as optimal as that of leucine for maintaining hydrophobic packing with nearby residues (e.g., Ala448, Lys444). Additionally, the consistently maintained hydrogen bond interaction between the backbone amide group of Leu489 and the carbonyl of Glu436 is lost due to the residue swap, potentially affecting the tertiary structure integrity.
c.1778T>A	L593H (3D Viewer)	GAP	Uncertain		1				-16.504	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.812	Likely Pathogenic	2.52	Destabilizing	0.2	2.32	Destabilizing	2.42	Destabilizing	2.75	Destabilizing	-6.77	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.77	Benign	0.00	Affected	3.37	35	-2	-3	-7.0	23.98	222.0	20.7	0.0	0.0	0.2	0.0		X					X	Potentially Pathogenic	The iso-propyl side chain of Leu593, located in an α helix (res. Glu582-Met603), packs favourably with multiple hydrophobic residues in the inter-helix space (e.g., Leu598, Ile589, Phe594, Phe561).In the variant simulations, His593 retains a similar packing arrangement via its aromatic imidazole ring. However, the polar nitrogen atoms introduce hydrogen bond donors and acceptors into the previously hydrophobic space. The epsilon protonated nitrogen of His593 forms a stable hydrogen bond with the phenol group of the Tyr505 side chain in an α helix (res. Gln503-Tyr518).While the residue swap could affect the tertiary assembly and the underlying protein folding process, it is difficult to determine if the mutation would be tolerated based solely on the variant simulations.
c.1404G>A	M468I (3D Viewer)	GAP				6-33438436-G-A	1	6.20e-7	-8.583	Likely Pathogenic	0.907	Likely Pathogenic	Ambiguous	0.508	Likely Pathogenic	2.53	Destabilizing	0.2	1.89	Ambiguous	2.21	Destabilizing	0.37	Likely Benign	-1.06	Neutral	0.748	Possibly Damaging	0.886	Possibly Damaging	-1.10	Pathogenic	0.07	Tolerated	3.37	31	1	2	2.6	-18.03
c.986G>A	R329H (3D Viewer)	C2	Uncertain		1	6-33437891-G-A	2	1.24e-6	-10.154	Likely Pathogenic	0.769	Likely Pathogenic	Likely Benign	0.155	Likely Benign	2.53	Destabilizing	0.7	0.71	Ambiguous	1.62	Ambiguous	0.82	Ambiguous	-3.17	Deleterious	0.995	Probably Damaging	0.778	Possibly Damaging	4.04	Benign	0.05	Affected	3.41	15	2	0	1.3	-19.05	220.4	81.4	0.1	0.1	0.2	0.3								Uncertain	The guanidinium group of Arg329, located at the end of an anti-parallel β sheet strand (res. Ala322-Asp330), faces the negatively charged lipid bilayer surface. While the residue swap does not cause any apparent negative effects on the protein structure in the variant simulations, it could adversely affect the SynGAP-membrane association in reality. The positively charged Arg329 side chain forms hydrogen bonds with other loop residues (e.g., Ser371, Asp338) that are expected to dynamically interact with the membrane head group region. However, this phenomenon is beyond the scope of the solvent-only simulations to unravel. Notably, histidine can also be double protonated and positively charged, but this alternative protonation state was not considered in the variant simulations.
c.2134G>T	G712C (3D Viewer)	GAP				6-33441599-G-T	1	6.20e-7	-11.376	Likely Pathogenic	0.829	Likely Pathogenic	Ambiguous	0.516	Likely Pathogenic	2.54	Destabilizing	0.0	5.72	Destabilizing	4.13	Destabilizing	0.56	Ambiguous	-7.75	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.31	Benign	0.00	Affected	3.50	9	-3	-3	2.9	46.09
c.821T>A	L274Q (3D Viewer)	C2	Uncertain		1				-15.518	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.774	Likely Pathogenic	2.54	Destabilizing	0.3	1.74	Ambiguous	2.14	Destabilizing	1.97	Destabilizing	-5.42	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	0.00	Pathogenic	0.00	Affected	3.38	19	-2	-2	-7.3	14.97	245.9	1.8	0.0	0.0	0.1	0.2	X		X				X	Potentially Pathogenic	The aliphatic side chain of Leu274, located in a β hairpin loop (res. Glu273-Lys278) connecting two anti-parallel β sheet strands, packs against multiple hydrophobic residues facing the β sheet (e.g., Ala271, Leu327, Tyr280, Val306). The hydrophilic carboxamide group of the Gln274 side chain is not suitable for this hydrophobic niche, causing nearby residues to adjust to make room for the hydrophilic glutamine. Additionally, a new hydrogen bond forms with the backbone carboxyl group of Arg272 in another β strand (res. Glu273-Arg259).As a result, the backbone amide group of Ala399 and the carbonyl group of Arg272, which connect two β strands at the β sheet end, form fewer hydrogen bonds in the variant than in the WT simulations. Although no major secondary structure disruption is observed in the variant simulations, the residue swap could profoundly affect the C2 domain folding, as the hydrophobic packing of Leu274 is crucial for maintaining the loop's contact with the rest of the C2 domain. Lastly, because the Leu274-containing loop faces the membrane surface, the residue swap could also negatively impact the SynGAP-membrane association.
c.1126G>T	G376C	C2	Uncertain		1				-7.686	In-Between	0.125	Likely Benign	Likely Benign	0.560	Likely Pathogenic	2.56	Destabilizing	0.5	0.22	Likely Benign	1.39	Ambiguous	0.16	Likely Benign	-1.15	Neutral	1.000	Probably Damaging	1.000	Probably Damaging	1.32	Pathogenic	0.01	Affected			-3	-3	2.9	46.09
c.680G>A	G227E (3D Viewer)	PH	Conflicting		2	6-33435531-G-A	3	1.86e-6	-9.186	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.792	Likely Pathogenic	2.56	Destabilizing	0.4	5.36	Destabilizing	3.96	Destabilizing	0.94	Ambiguous	-6.49	Deleterious	0.906	Possibly Damaging	0.360	Benign	5.72	Benign	0.01	Affected	3.43	12	0	-2	-3.1	72.06	237.7	-112.1	0.1	0.3	0.0	0.3		X				X		Uncertain	The introduced residue Glu227 is located in a β hairpin loop connecting two anti-parallel β sheet strands (res. Cys219-Thr224 and Thr228-Ala232). In the variant simulations, the carboxylate group of Glu227 frequently forms a salt bridge with the amino group of the neighboring residue Lys229. Despite this interaction, the integrity of the secondary structure element is not compromised. However, the β hairpins are potential nucleation sites during the initial stages of protein folding. Additionally, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.1169G>A	G390E (3D Viewer)	C2	Uncertain		1				-7.913	In-Between	0.645	Likely Pathogenic	Likely Benign	0.575	Likely Pathogenic	2.61	Destabilizing	0.9	4.28	Destabilizing	3.45	Destabilizing	0.47	Likely Benign	-0.87	Neutral	0.276	Benign	0.045	Benign	1.32	Pathogenic	0.05	Affected	4.32	8	0	-2	-3.1	72.06	241.5	-108.4	0.6	0.5	-0.1	0.1								Uncertain	Gly390 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. This loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play significant roles in protein functions that require flexibility, and so they are rich in glycine residues, prolines, and to a lesser extent, small hydrophilic residues to ensure maximum flexibility. Thus, the variant’s Glu390 may not be as well tolerated in the Ω loop. Additionally, the carboxylate group of Glu390 occasionally forms H-bonds with other loop residues in the variant simulations. The interaction between the acidic carboxylate side chain and the acidic membrane lipids may further influence the SynGAP-membrane complex. However, since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1084T>C	W362R (3D Viewer)	C2	Pathogenic		2				-14.004	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.706	Likely Pathogenic	2.64	Destabilizing	0.3	3.90	Destabilizing	3.27	Destabilizing	1.10	Destabilizing	-12.87	Deleterious	0.999	Probably Damaging	0.996	Probably Damaging	1.28	Pathogenic	0.00	Affected	3.39	24	2	-3	-3.6	-30.03	287.5	-34.1	-0.2	0.1	-0.6	0.2	X			X			X	Potentially Pathogenic	The indole ring of Trp362, located on the surface of an anti-parallel β sheet (res. Thr359-Pro364) in the C2 domain, stacks with nearby residues (e.g., Arg401, Arg272). In the variant simulations, the guanidinium group of the introduced residue Arg362 forms a salt bridge with the carboxylate group of Glu273 and, like Trp362, stacks with other arginine residues (e.g., Arg401, Arg272). This residue is at both the C2-membrane interface and the C2-RasGTPase interface, so the residue swap could potentially affect both interactions. However, these phenomena cannot be addressed using solvent-only simulations. Notably, Arg272, which stacks with both the non-mutated Trp362 and the mutated Arg362, forms a salt bridge directly with Asp105 of Ras in the WT simulations. Therefore, the residue swap could affect the C2 domain stability, the SynGAP-membrane association, and the SynGAP-Ras association.	10.1016/j.ajhg.2020.11.011
c.1402A>G	M468V (3D Viewer)	GAP	Uncertain		1				-9.461	Likely Pathogenic	0.361	Ambiguous	Likely Benign	0.570	Likely Pathogenic	2.69	Destabilizing	0.1	2.20	Destabilizing	2.45	Destabilizing	0.89	Ambiguous	-1.66	Neutral	0.998	Probably Damaging	0.993	Probably Damaging	-1.21	Pathogenic	0.08	Tolerated	3.37	31	1	2	2.3	-32.06
c.1942T>C	F648L		Uncertain		1				-9.296	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.468	Likely Benign	2.71	Destabilizing	0.8	2.08	Destabilizing	2.40	Destabilizing	1.04	Destabilizing	-5.98	Deleterious	0.999	Probably Damaging	0.976	Probably Damaging	3.45	Benign	0.08	Tolerated			2	0	1.0	-34.02
c.1037T>C	V346A (3D Viewer)	C2				6-33437942-T-C	1	6.20e-7	-8.556	Likely Pathogenic	0.856	Likely Pathogenic	Ambiguous	0.477	Likely Benign	2.72	Destabilizing	0.2	2.73	Destabilizing	2.73	Destabilizing	1.92	Destabilizing	-3.68	Deleterious	0.994	Probably Damaging	0.970	Probably Damaging	1.70	Pathogenic	0.01	Affected	3.37	25	0	0	-2.4	-28.05
c.1408A>G	M470V (3D Viewer)	GAP	Uncertain		1				-8.856	Likely Pathogenic	0.478	Ambiguous	Likely Benign	0.770	Likely Pathogenic	2.73	Destabilizing	0.1	1.88	Ambiguous	2.31	Destabilizing	1.31	Destabilizing	-3.58	Deleterious	0.999	Probably Damaging	0.993	Probably Damaging	-1.20	Pathogenic	0.15	Tolerated	3.37	34	1	2	2.3	-32.06
c.1971G>C	W657C	GAP	Uncertain		1				-12.035	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.463	Likely Benign	2.74	Destabilizing	0.3	1.69	Ambiguous	2.22	Destabilizing	1.30	Destabilizing	-11.06	Deleterious	1.000	Probably Damaging	0.982	Probably Damaging	3.43	Benign	0.03	Affected			-8	-2	3.4	-83.07
c.1214G>A	R405H (3D Viewer)	C2	Conflicting		2	6-33438119-G-A	4	2.48e-6	-9.081	Likely Pathogenic	0.713	Likely Pathogenic	Likely Benign	0.371	Likely Benign	2.79	Destabilizing	0.6	1.85	Ambiguous	2.32	Destabilizing	1.26	Destabilizing	-4.54	Deleterious	1.000	Probably Damaging	0.991	Probably Damaging	3.65	Benign	0.01	Affected	3.38	28	2	0	1.3	-19.05	214.0	102.2	-0.1	0.0	-0.7	0.1		X						Potentially Pathogenic	The guanidinium group of Arg405, located in an anti-parallel β sheet strand of the C2 domain (res. Pro398-Ile411), forms a salt bridge with the carboxylate group of the Glu446 side chain from an opposing α helix (res. Val441-Ser457) in the GAP domain. The positively charged Arg405 side chain also stacks with the aromatic ring of the Phe358 side chain from a loop preceding the β strand (res. Thr359-Thr366), which could assist in maintaining the anti-parallel strand arrangement.In the variant simulations, the imidazole ring of His405 does not stack with the aromatic ring of Phe358 nor form any lasting H-bonds with the loop residues. The imidazole ring of His405 (neutral and epsilon protonated in the simulations) is unable to form a salt bridge with Glu446, which could affect the tertiary structure assembly, although this is not apparent based on the variant simulations.
c.1115G>T	G372V (3D Viewer)	C2				6-33438020-G-T			-5.898	Likely Benign	0.126	Likely Benign	Likely Benign	0.535	Likely Pathogenic	2.81	Destabilizing	0.3	2.91	Destabilizing	2.86	Destabilizing	0.02	Likely Benign	-0.92	Neutral	0.003	Benign	0.000	Benign	-0.74	Pathogenic	0.06	Tolerated	3.52	18	-3	-1	4.6	42.08
c.1108G>A	G370S (3D Viewer)	C2	Uncertain		1	6-33438013-G-A	15	9.31e-6	-3.533	Likely Benign	0.081	Likely Benign	Likely Benign	0.282	Likely Benign	2.83	Destabilizing	2.0	1.05	Ambiguous	1.94	Ambiguous	-0.02	Likely Benign	0.47	Neutral	0.000	Benign	0.000	Benign	1.33	Pathogenic	0.77	Tolerated	3.42	19	1	0	-0.4	30.03	196.6	-49.6	0.9	2.2	-0.1	0.4								Uncertain	Gly370 is located in the Gly-rich Ω loop (res. Pro364- Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because, the Ω loop is assumed to be directly interacting with the membrane, it is only seen to move arbitrarily throughout the WT solvent simulations. The Ω loop is potentially playing a crucial loop in the SynGAP-membrane complex association, stability and dynamics, regardless, this aspect cannot be addressed through the solvent simulations only. The Ω-loops are known to have a major role in protein functions that requires flexibility and thus, they are rich in glycines, prolines and to a lesser extent, hydrophilic residues to ensure maximum flexibility. Thus, Ser370 in the variant is potentially tolerated in the Ω loop. However, since the effect on the Gly-rich Ω loop dynamics can only be well-studied through the SynGAP-membrane complex, no definite conclusions can be withdrawn.
c.1698G>T	K566N (3D Viewer)	GAP				6-33440750-G-T			-11.255	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.683	Likely Pathogenic	2.83	Destabilizing	0.3	1.33	Ambiguous	2.08	Destabilizing	1.32	Destabilizing	-4.04	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.43	Pathogenic	0.03	Affected	3.37	35	0	1	0.4	-14.07
c.1738G>A	G580S (3D Viewer)	GAP	Uncertain		1	6-33440790-G-A	1	6.20e-7	-10.788	Likely Pathogenic	0.861	Likely Pathogenic	Ambiguous	0.644	Likely Pathogenic	2.84	Destabilizing	0.2	0.59	Ambiguous	1.72	Ambiguous	0.87	Ambiguous	-5.73	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.23	Pathogenic	0.07	Tolerated	3.37	34	1	0	-0.4	30.03	233.9	-49.3	0.8	0.0	0.6	0.1						X		Potentially Benign	Gly580 is located on the outer surface in a short α-α loop turn connecting two α-helices (res. Arg563-Glu578, res. Glu582-Phe608) in the WT simulations. In the variant simulations, the side chain of Ser580 faces outward, and its hydroxyl group does not make any new or additional interactions compared to Gly580 in the WT simulations that could affect the protein structure.
c.2135G>A	G712D (3D Viewer)	GAP				6-33441600-G-A	1	6.20e-7	-8.211	Likely Pathogenic	0.946	Likely Pathogenic	Ambiguous	0.320	Likely Benign	2.87	Destabilizing	0.1	5.37	Destabilizing	4.12	Destabilizing	0.90	Ambiguous	-5.69	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	3.67	Benign	0.12	Tolerated	3.50	9	-1	1	-3.1	58.04
c.1159G>T	G387C (3D Viewer)	C2				6-33438064-G-T	1	6.21e-7	-7.609	In-Between	0.146	Likely Benign	Likely Benign	0.430	Likely Benign	2.88	Destabilizing	0.6	2.34	Destabilizing	2.61	Destabilizing	-0.03	Likely Benign	-0.58	Neutral	0.859	Possibly Damaging	0.346	Benign	1.32	Pathogenic	0.01	Affected	4.32	3	-3	-3	2.9	46.09
c.1762C>T	L588F (3D Viewer)	GAP				6-33440814-C-T			-14.050	Likely Pathogenic	0.987	Likely Pathogenic	Likely Pathogenic	0.736	Likely Pathogenic	2.90	Destabilizing	0.2	2.55	Destabilizing	2.73	Destabilizing	1.12	Destabilizing	-3.98	Deleterious	1.000	Probably Damaging	0.997	Probably Damaging	-1.38	Pathogenic	0.04	Affected	3.38	34	0	2	-1.0	34.02
c.872A>G	Y291C (3D Viewer)	C2	Uncertain		1				-8.997	Likely Pathogenic	0.967	Likely Pathogenic	Likely Pathogenic	0.505	Likely Pathogenic	2.90	Destabilizing	0.4	3.51	Destabilizing	3.21	Destabilizing	1.35	Destabilizing	-7.37	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.76	Pathogenic	0.01	Affected	3.38	23	0	-2	3.8	-60.04	205.2	66.1	0.1	0.0	-0.4	0.4	X						X	Potentially Pathogenic	The phenol group of the Tyr291 side chain, located in an anti-parallel β sheet strand (res. Met289-Pro298), packs against hydrophobic residues of the C2 and PH domains (e.g., Leu317, Leu286, Leu284, Pro208, Val209). The phenol ring of Tyr291 also forms favorable Met-aromatic stacking with the methyl group of Met289. In the variant simulation, the thiol group of the Cys291 side chain is not as suitable for the hydrophobic inter-domain space as the phenol ring of Tyr291. Consequently, the structural unity of the PH domain is weakened and ultimately unfolds in the second simulation. Moreover, the residue swap might result in severe detrimental effects on the C2 domain structure and the C2-PH domain tertiary structure assembly during folding.
c.1513T>C	Y505H (3D Viewer)	GAP	Likely Pathogenic		1				-11.383	Likely Pathogenic	0.982	Likely Pathogenic	Likely Pathogenic	0.646	Likely Pathogenic	2.91	Destabilizing	0.1	2.88	Destabilizing	2.90	Destabilizing	1.60	Destabilizing	-4.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.64	Benign	0.00	Affected	3.37	35	2	0	-1.9	-26.03
c.1786C>T	R596C (3D Viewer)	GAP	Uncertain		2	6-33440838-C-T	6	3.72e-6	-10.805	Likely Pathogenic	0.972	Likely Pathogenic	Likely Pathogenic	0.633	Likely Pathogenic	2.94	Destabilizing	0.0	1.49	Ambiguous	2.22	Destabilizing	-0.03	Likely Benign	-7.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.41	Pathogenic	0.00	Affected	3.37	35	-4	-3	7.0	-53.05	230.7	97.9	-0.1	0.0	-0.3	0.4		X		X				Potentially Pathogenic	The guanidinium group of Arg596, located in an α helix (res. Glu582-Met603), forms a salt bridge with the carboxylate group of Glu495 from another α helix (res. Leu489-Glu519). In the WT simulations, the side chain of Arg596 hydrogen bonds with the backbone carbonyl groups of Asn487, Glu486, Arg485, and Phe484. Additionally, Arg596 can hydrogen bond with the carboxamide group of the Asn487 side chain on an opposing loop that links two α helices (res. Ala461-Arg475, res. Leu489-Glu519).In the variant simulations, the thiol group of the Cys596 side chain is unable to form salt bridges or any of the hydrogen bonds that the Arg596 side chain can. Thus, the residue swap could affect the tertiary structure assembly more profoundly than observed in the simulations. Notably, Arg596 plays a key role in positioning the aforementioned loop, which is crucial for the placement of the “arginine finger” or the Arg485 side chain during RasGTPase activation.
c.1877T>C	I626T	GAP	Uncertain		1				-10.420	Likely Pathogenic	0.946	Likely Pathogenic	Ambiguous	0.640	Likely Pathogenic	2.94	Destabilizing	0.1	2.70	Destabilizing	2.82	Destabilizing	2.23	Destabilizing	-4.18	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.04	Benign	0.00	Affected			0	-1	-5.2	-12.05
c.1721T>C	L574P (3D Viewer)	GAP				6-33440773-T-C			-13.394	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.442	Likely Benign	2.95	Destabilizing	0.5	9.19	Destabilizing	6.07	Destabilizing	0.59	Ambiguous	-1.05	Neutral	1.000	Probably Damaging	0.971	Probably Damaging	-1.29	Pathogenic	0.26	Tolerated	3.38	32	-3	-3	-5.4	-16.04
c.758A>T	N253I (3D Viewer)	PH				6-33435609-A-T	1	6.20e-7	-15.241	Likely Pathogenic	0.970	Likely Pathogenic	Likely Pathogenic	0.836	Likely Pathogenic	2.95	Destabilizing	0.1	5.56	Destabilizing	4.26	Destabilizing	0.25	Likely Benign	-7.83	Deleterious	0.998	Probably Damaging	0.991	Probably Damaging	5.57	Benign	0.01	Affected	3.39	15	-3	-2	8.0	-0.94
c.1787G>A	R596H (3D Viewer)	GAP	Likely Benign		1	6-33440839-G-A	15	9.29e-6	-11.128	Likely Pathogenic	0.950	Likely Pathogenic	Ambiguous	0.717	Likely Pathogenic	3.00	Destabilizing	0.9	0.43	Likely Benign	1.72	Ambiguous	1.35	Destabilizing	-4.97	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.43	Pathogenic	0.00	Affected	3.37	35	2	0	1.3	-19.05	223.5	80.5	-0.1	0.0	-0.1	0.3		X		X				Potentially Pathogenic	The guanidinium group of Arg596, located in an α helix (res. Glu582-Met603), forms a salt bridge with the carboxylate group of Glu495 from another α helix (res. Leu489-Glu519). In the WT simulations, the side chain of Arg596 hydrogen bonds with the backbone carbonyl groups of Asn487, Glu486, Arg485, and Phe484. Additionally, Arg596 can hydrogen bond with the carboxamide group of the Asn487 side chain on an opposing loop that links two α helices (res. Ala461-Arg475, res. Leu489-Glu519).In the variant simulations, the imidazole ring of His596 can form hydrogen bonds with the same residues as arginine; however, these interactions are not as coordinated or strong in comparison. Thus, the residue swap could affect the tertiary structure assembly more profoundly than observed in the simulations. Notably, Arg596 plays a key role in positioning the aforementioned loop, which is crucial for the placement of the “arginine finger” or the Arg485 side chain during RasGTPase activation.
c.1025A>C	Y342S (3D Viewer)	C2	Uncertain		1				-7.996	In-Between	0.925	Likely Pathogenic	Ambiguous	0.407	Likely Benign	3.03	Destabilizing	0.1	2.87	Destabilizing	2.95	Destabilizing	0.93	Ambiguous	-6.60	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.75	Pathogenic	0.04	Affected	3.37	25	-3	-2	0.5	-76.10	200.1	77.8	0.0	0.0	-0.2	0.1								Potentially Pathogenic	The phenol ring of Tyr342, located at the end of an anti-parallel β sheet strand (res. Gly341-Pro349), faces outward in the C2 domain. In the WT simulations, the phenol ring of Tyr342 contributes to a triple tyrosine stack (Tyr342, Tyr328, and Tyr281) that links together three anti-parallel β sheet strands. Additionally, it shields Gly344 from the solvent, reducing its exposure and providing stability for the β-sandwich. This motif also contributes to a twist formation in the β sheet.In the variant simulations, the Ser342 side chain cannot participate in the stack formation. Instead, the hydroxyl group of the Ser342 side chain forms a hydrogen bond with the imidazole ring of His326 in a neighboring β strand (res. Ala322-Asp330). This disrupts the formation of a hydrogen bond between His326 and the carboxylate group of the Glu283 side chain from another β strand (res. Arg279-Cys285). Although these changes in surface interactions could weaken the characteristic twist that strengthens the β sheet fold, no major structural effects are observed in the variant simulations. The residue swap could also affect the SynGAP-membrane association, as the hydroxyl group of Ser342 could form hydrogen bonds with membrane-facing loop residues. However, this phenomenon cannot be addressed using solvent-only simulations.
c.743G>C	R248P (3D Viewer)	PH	Likely Pathogenic		1				-10.751	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.848	Likely Pathogenic	3.09	Destabilizing	0.6	8.87	Destabilizing	5.98	Destabilizing	1.21	Destabilizing	-5.97	Deleterious	0.998	Probably Damaging	0.878	Possibly Damaging	5.64	Benign	0.00	Affected	3.41	14	0	-2	2.9	-59.07	223.8	126.6	0.0	0.0	-0.2	0.1	X	X						Potentially Pathogenic	The guanidinium group of Arg248, located on an α helix (residues Ala236-Val250), forms two very stable salt bridges with Asp255 (from a short α helical section, res. Lys254-Asn256) and Glu244 (from a nearby loop) in the WT simulations. In the variant simulations, the pyrrolidine side chain of Pro248 cannot form any salt bridges, which could negatively affect the tertiary structure assembly of the PH domain. Additionally, Pro248 lacks a free amide group needed for hydrogen bonding with the backbone carbonyl group of Asn245, disrupting the continuity of the α helix.
c.1214G>C	R405P (3D Viewer)	C2	Uncertain		1				-14.206	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.572	Likely Pathogenic	3.11	Destabilizing	0.3	5.19	Destabilizing	4.15	Destabilizing	1.26	Destabilizing	-6.32	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.62	Benign	0.01	Affected	3.38	28	-2	0	2.9	-59.07
c.1082A>C	Q361P (3D Viewer)	C2	Likely Pathogenic		1				-13.280	Likely Pathogenic	0.956	Likely Pathogenic	Likely Pathogenic	0.482	Likely Benign	3.12	Destabilizing	0.0	3.45	Destabilizing	3.29	Destabilizing	0.38	Likely Benign	-3.03	Deleterious	0.996	Probably Damaging	0.979	Probably Damaging	1.63	Pathogenic	0.05	Affected	3.37	25	-1	0	1.9	-31.01
c.844T>C	C282R (3D Viewer)	C2	Pathogenic		2				-16.378	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.466	Likely Benign	3.13	Destabilizing	0.6	1.58	Ambiguous	2.36	Destabilizing	1.70	Destabilizing	-11.03	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	1.63	Pathogenic	0.00	Affected	3.39	18	-4	-3	-7.0	53.05	297.4	-98.2	-0.1	0.1	0.5	0.0	X		X				X	Potentially Pathogenic	The thiol-containing side chain of Cys282, located at the beginning of an anti-parallel β sheet strand (res. Arg279-Leu286), is packed against multiple hydrophobic residues (e.g., Ile268, Leu284, Trp308, Leu327). In the variant simulations, the bulky side chain of Arg282 with its positively charged guanidinium group is not suitable for this hydrophobic niche. Consequently, the hydrophobic residues must either make room to accommodate Arg282 or it must escape the hydrophobic C2 domain core.As a result, new hydrogen bonds are formed with the backbone carbonyl groups of the surrounding β sheet residues Ala399, Leu325, and His326, which decreases the unity of the secondary structure elements. Notably, it is likely that the residue swap causes major problems during the C2 domain folding that are not visible in the variant simulations. In fact, even increased lability in the C2 domain could adversely affect the establishment of a stable SynGAP-membrane association.
c.1282T>C	Y428H (3D Viewer)	GAP				6-33438187-T-C	1	6.19e-7	-8.566	Likely Pathogenic	0.961	Likely Pathogenic	Likely Pathogenic	0.458	Likely Benign	3.18	Destabilizing	0.1	2.20	Destabilizing	2.69	Destabilizing	1.80	Destabilizing	-4.77	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.40	Benign	0.04	Affected	3.38	25	2	0	-1.9	-26.03
c.1409T>C	M470T (3D Viewer)	GAP	Uncertain		1				-8.104	Likely Pathogenic	0.976	Likely Pathogenic	Likely Pathogenic	0.763	Likely Pathogenic	3.19	Destabilizing	0.1	2.68	Destabilizing	2.94	Destabilizing	1.49	Destabilizing	-5.30	Deleterious	0.996	Probably Damaging	0.985	Probably Damaging	-1.08	Pathogenic	0.24	Tolerated	3.37	34	-1	-1	-2.6	-30.09	213.8	46.5	0.0	0.0	-0.2	0.2		X					X	Potentially Pathogenic	The thioether group of Met470, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues in the inter-helix space (e.g., Val473, Leu558, Cys576, Trp572) formed by two other α helices (res. Ser604–Arg581, res. Pro562–Arg579). In the WT simulations, the Met470 side chain also packs against the positively charged guanidinium groups of Arg575, Arg429, and Arg579, which form salt bridges with the negatively charged carboxylate groups of the Asp474 and Asp467 side chains at the protein surface. In the variant simulations, the hydroxyl group of the Thr470 side chain forms an H-bond with the backbone carbonyl group of Ser466 in the α helix, potentially lowering its structural integrity. Importantly, the hydroxyl group of Thr470 also forms an H-bond with the guanidinium group of Arg575, which helps it form a more permanent salt bridge with Asp467.
c.1403T>A	M468K (3D Viewer)	GAP	Likely Pathogenic		1				-16.982	Likely Pathogenic	0.978	Likely Pathogenic	Likely Pathogenic	0.828	Likely Pathogenic	3.21	Destabilizing	0.1	3.30	Destabilizing	3.26	Destabilizing	2.57	Destabilizing	-4.61	Deleterious	0.878	Possibly Damaging	0.922	Probably Damaging	-1.34	Pathogenic	0.04	Affected	3.37	31	0	-1	-5.8	-3.02	188.7	69.3	0.0	0.0	-0.1	0.2			X				X	Potentially Pathogenic	The thioether group of Met468, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues (e.g., Phe464, Leu465, Leu489) in an inter-helix space formed by two other α helices (res. Ala461–Phe476, res. Thr488–Gly502). In the variant simulations, the positively charged side chain of Lys468 rotates outward to escape the hydrophobic niche, forming an H-bond with the hydroxyl group of the Ser471 side chain and a salt bridge with the carboxylate group of the Glu472 side chain. This residue swap also disrupts the methionine-aromatic stacking with the phenyl ring of the Phe464 side chain. Although no large-scale structural changes are observed during the variant simulations, the importance of hydrophobic packing suggests that the effects could be more pronounced during protein folding.
c.2075T>A	L692Q (3D Viewer)	GAP	Uncertain		1				-13.873	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.596	Likely Pathogenic	3.24	Destabilizing	0.1	3.27	Destabilizing	3.26	Destabilizing	2.76	Destabilizing	-5.98	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	3.06	Benign	0.00	Affected	3.42	17	-2	-2	-7.3	14.97
c.1957C>G	L653V	GAP	Uncertain		1				-7.050	In-Between	0.301	Likely Benign	Likely Benign	0.146	Likely Benign	3.28	Destabilizing	0.3	2.18	Destabilizing	2.73	Destabilizing	1.32	Destabilizing	-2.25	Neutral	0.227	Benign	0.039	Benign	3.28	Benign	0.08	Tolerated			2	1	0.4	-14.03
c.2050G>C	D684H (3D Viewer)	GAP	Uncertain		1				-14.194	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.613	Likely Pathogenic	3.36	Destabilizing	1.0	2.95	Destabilizing	3.16	Destabilizing	0.55	Ambiguous	-6.98	Deleterious	1.000	Probably Damaging	0.972	Probably Damaging	3.36	Benign	0.00	Affected	3.42	17	-1	1	0.3	22.05
c.1703T>G	V568G (3D Viewer)	GAP				6-33440755-T-G			-15.135	Likely Pathogenic	0.938	Likely Pathogenic	Ambiguous	0.933	Likely Pathogenic	3.39	Destabilizing	0.1	4.45	Destabilizing	3.92	Destabilizing	2.34	Destabilizing	-6.81	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.46	Pathogenic	0.00	Affected	3.37	35	-3	-1	-4.6	-42.08
c.968T>C	L323P (3D Viewer)	C2							-12.507	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.762	Likely Pathogenic	3.39	Destabilizing	0.6	8.46	Destabilizing	5.93	Destabilizing	2.20	Destabilizing	-4.80	Deleterious	0.999	Probably Damaging	0.977	Probably Damaging	0.59	Pathogenic	0.01	Affected	4.29	398	-3	-3	-5.4	-16.04	201.9	68.2	0.0	0.1	0.6	0.3	X							Potentially Pathogenic	The iso-butyl side chain of Leu323, located at the beginning of an anti-parallel β sheet strand (res. Ala322-Asp330), packs against multiple hydrophobic leucine residues (e.g., Leu264, Leu266, Leu284, Leu286). In contrast, in the variant simulations, the less bulky cyclic five-membered pyrrolidine ring of Pro323 cannot fill the hydrophobic space as effectively as the branched hydrocarbon side chain of leucine. Notably, the backbone amide group of Leu323 forms a hydrogen bond with the backbone carbonyl group of Cys285. Pro323 cannot form this bond due to the absence of the backbone amide group, resulting in partial unfolding of the anti-parallel β sheet end in the variant simulations.
c.1813C>T	P605S (3D Viewer)	GAP	Uncertain		1				-10.830	Likely Pathogenic	0.987	Likely Pathogenic	Likely Pathogenic	0.718	Likely Pathogenic	3.40	Destabilizing	0.1	3.34	Destabilizing	3.37	Destabilizing	1.00	Destabilizing	-7.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	0.70	Pathogenic	0.00	Affected	3.37	35	1	-1	0.8	-10.04	213.8	-15.4	-0.3	0.2	0.2	0.1				X			X	Potentially Pathogenic	Pro605 is located in a short turn between an α helix (res. Glu582-Met603) and a short α helical section (res. Ser606-Phe608). The pyrrolidine side chain of Pro605 packs hydrophobically with nearby hydrophobic residues (e.g., Ile514, Leu623, Leu610) in the inter-helix space. Additionally, proline lacks a free backbone amide group, which breaks the α helix and facilitates the turn in the WT structure.In the variant simulations, the hydroxyl side chain of Ser605 forms hydrogen bonds with the backbone carbonyl groups of Ala601 and Ile602. Importantly, the helix end is more stable than with Pro605 in the WT. Indeed, proline is a more effective secondary structure breaker compared to serine.Thus, the residue swap could have a more profound effect on the actual folding process, for example, by preventing the bending at the α helix end, than what the simulations suggest. Moreover, due to its location at the GAP-Ras interface, the residue swap could affect the GAP-Ras association.
c.1162G>A	G388S (3D Viewer)	C2				6-33438067-G-A	1	6.21e-7	-5.036	Likely Benign	0.089	Likely Benign	Likely Benign	0.446	Likely Benign	3.42	Destabilizing	3.5	1.69	Ambiguous	2.56	Destabilizing	0.18	Likely Benign	-0.52	Neutral	0.980	Probably Damaging	0.968	Probably Damaging	1.33	Pathogenic	0.05	Affected	4.32	3	0	1	-0.4	30.03
c.791T>A	L264Q (3D Viewer)	C2	Uncertain		1				-15.729	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.678	Likely Pathogenic	3.43	Destabilizing	0.1	2.41	Destabilizing	2.92	Destabilizing	2.48	Destabilizing	-5.52	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	0.49	Pathogenic	0.00	Affected	3.38	18	-2	-2	-7.3	14.97	254.7	-7.6	0.0	0.0	0.0	0.3	X		X				X	Potentially Pathogenic	The iso-butyl branched hydrocarbon side chain of Leu264, located at the end of an anti-parallel β sheet strand (res. Arg259-Arg272), packs against multiple hydrophobic residues such as Leu266, Phe314, Leu317, and Leu323 in the WT simulations. In the variant simulations, the hydrophilic carboxamide group of the Gln264 side chain is not suitable for the hydrophobic niche, causing the hydrophobic residues to make room for the swapped residue. Additionally, the carboxamide group of Gln264 forms hydrogen bonds with the backbone amide groups of Arg405 and Lys256 in the β sheet and the carbonyl group of Val350 in an α helical section of a nearby loop (res. Pro359-Phe358). The residue swap disrupts the packing of the C2 domain, which could adversely affect the C2 domain structure during folding. This disruption could potentially weaken the stability of the SynGAP-membrane association.
c.1403T>C	M468T (3D Viewer)	GAP	Uncertain		2	6-33438435-T-C	1	6.20e-7	-12.399	Likely Pathogenic	0.862	Likely Pathogenic	Ambiguous	0.801	Likely Pathogenic	3.47	Destabilizing	0.1	3.10	Destabilizing	3.29	Destabilizing	1.84	Destabilizing	-3.85	Deleterious	0.994	Probably Damaging	0.985	Probably Damaging	-1.31	Pathogenic	0.01	Affected	3.37	31	-1	-1	-2.6	-30.09	214.6	47.1	0.0	0.0	0.1	0.0							X	Potentially Pathogenic	The thioether group of Met468, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues (e.g., Phe464, Leu465, Leu489) in an inter-helix space formed by two other α helices (res. Ala461–Phe476, res. Thr488–Gly502). In the variant simulations, the hydrophilic side chain of Thr468 does not pack favorably in the hydrophobic niche, and the methionine-aromatic stacking is lost. Although the hydroxyl group of Thr468 forms an H-bond with the backbone carbonyl group of Phe464, the integrity of the α helix is not affected in the simulations. No large-scale structural changes are observed during the variant simulations; however, due to the importance of hydrophobic packing, the effects could be more pronounced during protein folding.
c.2131C>G	L711V (3D Viewer)	GAP	Uncertain		1	6-33441596-C-G	1	6.20e-7	-10.045	Likely Pathogenic	0.709	Likely Pathogenic	Likely Benign	0.170	Likely Benign	3.48	Destabilizing	0.1	2.22	Destabilizing	2.85	Destabilizing	1.40	Destabilizing	-2.59	Deleterious	0.992	Probably Damaging	0.970	Probably Damaging	3.34	Benign	0.00	Affected	3.50	9	1	2	0.4	-14.03
c.1187G>T	G396V (3D Viewer)	C2				6-33438092-G-T	6	3.72e-6	-5.663	Likely Benign	0.120	Likely Benign	Likely Benign	0.332	Likely Benign	3.49	Destabilizing	1.7	5.28	Destabilizing	4.39	Destabilizing	0.34	Likely Benign	-2.56	Deleterious	0.062	Benign	0.014	Benign	3.90	Benign	0.24	Tolerated	3.41	15	-3	-1	4.6	42.08
c.1685C>T	P562L (3D Viewer)	GAP	Conflicting		10	6-33440737-C-T			-13.438	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.829	Likely Pathogenic	3.54	Destabilizing	0.8	0.17	Likely Benign	1.86	Ambiguous	-0.14	Likely Benign	-9.95	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	0.58	Pathogenic	0.00	Affected	3.37	35	-3	-3	5.4	16.04	228.8	-68.5	-0.1	0.0	0.1	0.2							X	Potentially Pathogenic	Pro562 is located on an α-α loop between two α-helices (res. Ala533-Val560 and res. Arg563-Glu578). The cyclic pyrrolidine side chain of Pro562 hydrophobically packs with other residues in the inter-helix space, such as Leu565, Ile501, and Phe561. In the variant simulations, Leu562 packs more favorably with the nearby hydrophobic residues, and the backbone amide group of Leu562 (absent in proline) does not form any intra-protein hydrogen bonds. However, prolines are well-suited for unstructured regions like loops, and thus, Pro562 in the WT is necessary at the end of the helix to induce a tight turn during folding. Although no negative structural effects are observed during the simulations, the residue swap could potentially cause extensive damage to the protein structure during folding.	10.1016/j.ajhg.2020.11.011
c.2143C>T	P715S (3D Viewer)	GAP	Likely Pathogenic		1	6-33441608-C-T	1	6.20e-7	-7.635	In-Between	0.787	Likely Pathogenic	Ambiguous	0.277	Likely Benign	3.54	Destabilizing	0.0	0.81	Ambiguous	2.18	Destabilizing	0.94	Ambiguous	-7.17	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	3.43	Benign	0.01	Affected	3.50	9	1	-1	0.8	-10.04	231.8	-14.0	-0.1	0.0	-0.8	0.1							X	Uncertain	Pro715, along with Gly712 and Pro713, are located in a hinge region of an α-helix making a ~90-degree turn (res. Lys705-Leu725). In the WT simulations, the pyrrolidine side chain of Pro715, lacking the backbone amide groups altogether, forces the tight helix turn to take place while also hydrophobically packing with nearby residues (e.g., Leu700, Leu708, Leu714, and Leu718). Leu715, with a normal amide backbone, could potentially affect protein folding and turn formation, although this was not observed in the variant simulations. Additionally, the hydroxyl group of the Ser715 side chain can form hydrogen bonds with the backbone carbonyl group of Gly712 and disrupt the hydrophobic packing arrangement of the leucine residues from the neighboring α-helices, impacting the GAP domain tertiary assembly.
c.1160G>A	G387D (3D Viewer)	C2				6-33438065-G-A	2	1.24e-6	-8.625	Likely Pathogenic	0.612	Likely Pathogenic	Likely Benign	0.459	Likely Benign	3.57	Destabilizing	2.3	3.22	Destabilizing	3.40	Destabilizing	0.39	Likely Benign	-0.37	Neutral	0.069	Benign	0.041	Benign	1.32	Pathogenic	0.02	Affected	4.32	3	-1	1	-3.1	58.04
c.1390T>G	F464V (3D Viewer)	GAP	Uncertain		1				-12.254	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.592	Likely Pathogenic	3.61	Destabilizing	0.1	2.89	Destabilizing	3.25	Destabilizing	1.40	Destabilizing	-6.96	Deleterious	0.998	Probably Damaging	0.996	Probably Damaging	3.36	Benign	0.04	Affected	3.37	34	-1	-1	1.4	-48.04	210.1	40.5	-0.1	0.0	-0.9	0.3							X	Potentially Pathogenic	The phenyl ring of Phe464, located in the middle of an α helix (res. Ala461–Phe476), packs against hydrophobic residues (e.g., Met468, Leu451, Leu455, and Tyr428) in the inter-helix space formed with two other α helices (res. Asn440-Lys460 and res. Pro413-Glu436). The iso-propyl side chain of Val464 is similarly hydrophobic but considerably smaller than the original phenyl ring of Phe464. To compensate for the size difference, neighboring residues need to fill in the gap in the variant simulations.The phenolic side chain of Tyr428, located at the middle bend of an α helix (res. Glu436-Pro413), assumes a new position in the inter-helix space or rotates inward next to the third α helix (res. Asn440-Lys460) when the stable H-bond between Tyr428 and Asp467 seen in the WT simulations breaks. The residue swap also leads to the loss of the methionine-aromatic interaction between the Met468 and Phe464 side chains, which could weaken the integrity of the parent α helix (res. Ala461-Phe476). Although the simulations likely underestimate the full adverse effect of the introduced mutation during folding, the two opposing α helices (res. Ala461–Phe476 and res. Glu436-Pro413) move substantially closer to each other in the variant simulations.
c.1979T>C	M660T (3D Viewer)	GAP				6-33441238-T-C	1	6.20e-7	-9.791	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.561	Likely Pathogenic	3.62	Destabilizing	0.1	2.05	Destabilizing	2.84	Destabilizing	1.91	Destabilizing	-5.99	Deleterious	0.967	Probably Damaging	0.633	Possibly Damaging	3.36	Benign	0.02	Affected	3.38	28	-1	-1	-2.6	-30.09
c.878G>C	R293P (3D Viewer)	C2	Likely Pathogenic		1				-16.275	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.497	Likely Benign	3.62	Destabilizing	0.4	9.06	Destabilizing	6.34	Destabilizing	0.47	Likely Benign	-6.43	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.45	Pathogenic	0.01	Affected	3.38	23	0	-2	2.9	-59.07	202.3	132.0	0.1	0.0	0.1	0.1	X	X		X				Potentially Pathogenic	The guanidinium group of the Arg293 side chain, located in an anti-parallel β sheet strand (res. Met289-Pro298), packs against the phenol ring of the Tyr281 side chain or forms a salt bridge with the carboxylate group of Glu283 on the outer side of the C2 domain. In the WT simulations, the positively charged side chain of arginine remains outside the hydrophobic C2 domain, resulting in a twist in the β strand. The backbone amide bond of Arg293 potentially maintains this twist by forming a hydrogen bond with the carbonyl group of His210 or the hydroxyl group of Ser211 in the anti-parallel β sheet.Although this twist is also maintained in the variant simulations, replacing the positively charged residue with proline, which lacks the backbone amide group altogether, causes the β strand to unfold. Because Arg293 is positioned at the C2 and PH domain interface, the residue swap could significantly impact the tertiary structure assembly. Notably, Arg293 is located at the SynGAP-Ras interface, and its role in complex formation cannot be fully understood through solvent-only simulations.
c.1367A>C	Q456P (3D Viewer)	GAP	Uncertain		1				-15.250	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.469	Likely Benign	3.68	Destabilizing	0.2	8.43	Destabilizing	6.06	Destabilizing	0.82	Ambiguous	-5.66	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	3.34	Benign	0.07	Tolerated	3.37	34	-1	0	1.9	-31.01
c.1151G>T	G384V (3D Viewer)	C2				6-33438056-G-T			-6.968	Likely Benign	0.131	Likely Benign	Likely Benign	0.460	Likely Benign	3.69	Destabilizing	0.4	6.77	Destabilizing	5.23	Destabilizing	-0.11	Likely Benign	-1.01	Neutral	0.994	Probably Damaging	0.990	Probably Damaging	1.32	Pathogenic	0.01	Affected	4.32	2	-3	-1	4.6	42.08
c.1157G>A	G386E (3D Viewer)	C2	Uncertain		1	6-33438062-G-A			-9.286	Likely Pathogenic	0.685	Likely Pathogenic	Likely Benign	0.447	Likely Benign	3.69	Destabilizing	2.9	0.79	Ambiguous	2.24	Destabilizing	0.54	Ambiguous	-0.83	Neutral	0.860	Possibly Damaging	0.354	Benign	3.93	Benign	0.01	Affected	4.32	3	-2	0	-3.1	72.06
c.1199T>A	V400E (3D Viewer)	C2	Uncertain		1				-13.686	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.810	Likely Pathogenic	3.70	Destabilizing	0.2	2.46	Destabilizing	3.08	Destabilizing	2.29	Destabilizing	-4.88	Deleterious	0.920	Possibly Damaging	0.335	Benign	5.31	Benign	0.00	Affected	3.38	27	-2	-2	-7.7	29.98	249.1	-38.8	-0.1	0.1	1.0	0.0	X		X				X	Potentially Pathogenic	The iso-propyl side chain of Val400, located in an anti-parallel β sheet strand (res. Ala399-Ile411), hydrophobically packs against hydrophobic residues within the anti-parallel β sheet of the C2 domain (e.g., Ile268, Ala404, Leu325, Leu402). In the variant simulations, the negatively charged carboxylate group of the Glu400 side chain is not suitable for occupying the hydrophobic niche. Consequently, the side chain escapes the center of the C2 domain and interacts with the backbone amide groups of Leu402 in the same β strand and/or Ile269 and Glu270 in a neighboring β strand (res. Arg259-Arg272). This residue swap disrupts the hydrophobic packing and generally has extensive negative effects on the C2 domain structure. At a minimum, the residue swap could affect the C2 domain stability and membrane association.
c.1991T>C	L664S (3D Viewer)	GAP	Likely Benign		1	6-33441250-T-C	1	6.20e-7	-16.498	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.543	Likely Pathogenic	3.75	Destabilizing	0.2	3.63	Destabilizing	3.69	Destabilizing	2.77	Destabilizing	-5.99	Deleterious	1.000	Probably Damaging	0.996	Probably Damaging	2.85	Benign	0.00	Affected	3.38	28	-3	-2	-4.6	-26.08	215.5	50.1	0.0	0.0	-0.2	0.2						X		Potentially Benign	The iso-butyl side chain of L664, located on an α-helix (res. Ser641-Glu666), hydrophobically interacts with residues in the inter-helix space between three helices (res. Glu617-Asn635, res. Glu582-Met603, and res. Ser641-Glu666), such as Ile589, Phe663, and Met660. In the variant simulations, the hydroxyl group of Ser664 forms hydrogen bonds with the backbone carbonyl oxygen of another helix residue, such as Met660 or Gln661. This interaction is known to destabilize hydrogen bonding in the α-helix, but this effect was not observed in the simulations. Additionally, Ser664 occasionally forms hydrogen bonds with the carboxylate group of Asp586 on another α-helix (res. Glu582-Met603), which could minimally influence the tertiary structure assembly. Despite these interactions, no major negative effects on the protein structure were observed during the simulations.
c.968T>G	L323R (3D Viewer)	C2	Likely Pathogenic		1				-14.568	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.692	Likely Pathogenic	3.75	Destabilizing	0.4	4.47	Destabilizing	4.11	Destabilizing	2.15	Destabilizing	-4.70	Deleterious	0.999	Probably Damaging	0.969	Probably Damaging	0.59	Pathogenic	0.01	Affected	3.39	22	-3	-2	-8.3	43.03	261.8	-61.6	-0.4	0.2	0.8	0.2	X		X				X	Potentially Pathogenic	The iso-butyl side chain of Leu323, located at the beginning of an anti-parallel β sheet strand (res. Ala322-Asp330), packs against multiple hydrophobic leucine residues (e.g., Leu264, Leu266, Leu284, Leu286). In contrast, in the variant simulations, the positively charged guanidinium group of the Arg323 side chain is unsuitable for the hydrophobic niche. Consequently, the side chain either rotates away from the center of the C2 domain or, if it remains within the C2 domain core, it reorients nearby residues to form hydrogen bonds. Regardless, the residue swap extensively disrupts the C2 domain structure.
c.1790T>G	F597C (3D Viewer)	GAP				6-33440842-T-G	1	6.19e-7	-12.099	Likely Pathogenic	0.988	Likely Pathogenic	Likely Pathogenic	0.953	Likely Pathogenic	3.77	Destabilizing	0.2	4.17	Destabilizing	3.97	Destabilizing	1.97	Destabilizing	-7.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-2.19	Pathogenic	0.00	Affected	3.37	35	-2	-4	-0.3	-44.04
c.1771G>C	A591P (3D Viewer)	GAP	Uncertain		1				-14.479	Likely Pathogenic	0.991	Likely Pathogenic	Likely Pathogenic	0.404	Likely Benign	3.78	Destabilizing	0.3	7.29	Destabilizing	5.54	Destabilizing	1.45	Destabilizing	-4.41	Deleterious	0.995	Probably Damaging	0.853	Possibly Damaging	3.35	Benign	0.01	Affected	3.37	35	1	-1	-3.4	26.04	191.5	-10.1	0.2	0.1	0.4	0.1	X							Potentially Pathogenic	The methyl group of the Ala591 side chain, located in the middle of an α helix (res. Glu582-Met603), packs against hydrophobic residues (e.g., Ile483, Phe484) of an opposing partially helical loop (res. Phe476-Asn487).In the variant simulations, Pro591 lacks a free backbone amide group and, therefore, cannot form a hydrogen bond with the backbone carbonyl of Arg587 as Ala591 does in the WT. This notably weakens the α helix integrity and compromises the continuity of the helix. In reality, the effect on the structure during protein folding could be more severe.
c.1505G>A	G502D (3D Viewer)	GAP	Uncertain		1				-14.796	Likely Pathogenic	0.994	Likely Pathogenic	Likely Pathogenic	0.915	Likely Pathogenic	3.79	Destabilizing	0.9	5.69	Destabilizing	4.74	Destabilizing	1.38	Destabilizing	-6.80	Deleterious	0.999	Probably Damaging	0.977	Probably Damaging	-1.66	Pathogenic	0.00	Affected	3.37	35	1	-1	-3.1	58.04	224.2	-80.0	-0.8	0.7	0.6	0.3	X		X				X	Potentially Pathogenic	Gly502 is located in a hinge in the middle of an α-helix (res. Leu489-Glu519). In the WT, Gly502 acts as an α-helix breaker due to its lack of a side chain, facilitating a bend in the middle of the α-helix. In the variant simulations, the carboxylate group of Asp502 forms hydrogen bonds with neighboring residues (e.g., Ser677, Lys504), disrupting the hinge. Additionally, Asp502 struggles to fit into the α-helix hinge and cannot generate a similar bend as Gly502, which would drastically affect the secondary structure during folding. Thus, the deleterious effect seen in the simulations is likely an underestimate of the impact of the residue swap on the protein structure during protein folding.
c.1681T>A	F561I (3D Viewer)	GAP				6-33440733-T-A	1	6.32e-7	-11.708	Likely Pathogenic	0.990	Likely Pathogenic	Likely Pathogenic	0.710	Likely Pathogenic	3.82	Destabilizing	0.1	2.13	Destabilizing	2.98	Destabilizing	1.46	Destabilizing	-5.97	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	-1.06	Pathogenic	0.09	Tolerated	3.37	35	0	1	1.7	-34.02
c.1349C>A	A450E (3D Viewer)	GAP	Uncertain		1				-16.578	Likely Pathogenic	0.989	Likely Pathogenic	Likely Pathogenic	0.653	Likely Pathogenic	3.86	Destabilizing	0.2	5.23	Destabilizing	4.55	Destabilizing	1.59	Destabilizing	-4.67	Deleterious	0.999	Probably Damaging	0.992	Probably Damaging	3.38	Benign	0.07	Tolerated	3.37	32	0	-1	-5.3	58.04	240.1	-82.6	0.0	0.0	0.7	0.0			X				X	Potentially Pathogenic	The methyl group of Ala450, located in an α helix (res. Asn440-Thr458), packs against hydrophobic residues in the inter-helix space (e.g., Leu692). In the variant simulations, the carboxylate group of the Glu450 side chain rotates outward, away from the hydrophobic niche, where it does not form any lasting salt bridges or H-bonds. Although the residue swap does not negatively affect the protein structure based on the simulations, it is possible that the introduction of the negatively charged residue adversely affects the folding process or tertiary assembly.
c.1490A>G	Y497C (3D Viewer)	GAP	Uncertain		1				-11.872	Likely Pathogenic	0.948	Likely Pathogenic	Ambiguous	0.806	Likely Pathogenic	3.88	Destabilizing	0.1	4.76	Destabilizing	4.32	Destabilizing	1.40	Destabilizing	-8.82	Deleterious	1.000	Probably Damaging	0.995	Probably Damaging	-1.65	Pathogenic	0.03	Affected	3.37	35	0	-2	3.8	-60.04	209.9	59.1	-0.1	0.0	-0.3	0.1		X					X	Potentially Pathogenic	Tyr497 is located in the α-helix (res. Leu489-Glu519) within the inter-helix space of four α-helices (res. Leu489-Ile501, res. Val441-Ser457, res. Arg563-Glu578, res. Ala461-Val473). In the WT simulations, the phenol ring of Tyr497 hydrophobically packs with other residues in the inter-helix space (e.g., Leu465, Leu565, Val568). The hydroxyl group of Tyr497 also alternately forms hydrogen bonds with the carboxylate side chain of Gln456 and the backbone carbonyl of Glu564. Thus, Tyr497 plays a role in the folding and maintenance of the tertiary structure assembly between these four helices.In the variant simulations, the comparatively smaller residue, Cys497, cannot maintain any of the interactions seen with Tyr497 in the WT. Although no severe deleterious consequences are observed in the simulations, the structural effects could be more pronounced during actual protein folding. Indeed, the tertiary structure is seen to slightly break apart in the variant simulations.
c.2162T>G	I721S (3D Viewer)	GAP	Uncertain		1				-14.032	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.466	Likely Benign	3.91	Destabilizing	0.1	3.96	Destabilizing	3.94	Destabilizing	2.28	Destabilizing	-5.26	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.21	Pathogenic	0.00	Affected	3.50	9	-1	-2	-5.3	-26.08	203.3	49.3	-0.1	0.0	-1.1	0.0							X	Uncertain	The sec-butyl side chain of Ile721, located on an α-helix (res. Leu714-Arg726), engages in hydrophobic packing with other residues in the hydrophobic inter-helix space, such as Phe420, Tyr417, His693, and Leu717. In the variant simulations, the hydroxyl side chain of Ser721 forms hydrogen bonds with nearby residues, such as Leu717 and His693. Although no major structural changes are observed during the variant simulations, the hydrophilic residue Ser721 could disrupt the hydrophobic packing during folding. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.1142G>C	G381A (3D Viewer)	C2				6-33438047-G-C	1	6.23e-7	-6.266	Likely Benign	0.103	Likely Benign	Likely Benign	0.507	Likely Pathogenic	3.97	Destabilizing	0.7	2.05	Destabilizing	3.01	Destabilizing	0.06	Likely Benign	-0.63	Neutral	0.718	Possibly Damaging	0.332	Benign	1.33	Pathogenic	0.52	Tolerated	4.32	9	0	1	2.2	14.03
c.896G>A	R299H (3D Viewer)	C2	Conflicting		2	6-33437801-G-A	10	6.20e-6	-7.731	In-Between	0.388	Ambiguous	Likely Benign	0.238	Likely Benign	3.97	Destabilizing	1.0	0.94	Ambiguous	2.46	Destabilizing	1.41	Destabilizing	-3.35	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	1.69	Pathogenic	0.02	Affected	3.39	19	2	0	1.3	-19.05	211.2	72.5	-0.1	0.2	-0.2	0.3	X							Potentially Pathogenic	The guanidinium group of Arg299, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Met289-Pro298, res. Thr305-Asn315), forms hydrogen bonds that stabilize the tight turn. In the WT simulations, the Arg299 side chain hydrogen bonds with the loop backbone carbonyl groups (e.g., Ser302, Thr305, Leu274, Gly303), the hydroxyl group of Ser300, and even forms a salt bridge with the carboxylate group of Asp304.In the variant simulations, the imidazole ring of His299 (epsilon protonated state) hydrogen bonds with the carbonyl group of Asp304 and the hydroxyl group of Ser300. However, it does not form as many or as strong interactions as arginine, which could affect the initial formation of the secondary hairpin loop during folding. β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant.Additionally, His299 prefers to hydrophobically interact with other hydrophobic residues inside the C2 domain core (e.g., Val306, Leu274), which destabilizes the C2 domain. Indeed, the β strand partially unfolds during the second simulation. Moreover, the positively charged Arg299 side chain faces the polar head group region of the inner leaflet membrane and could directly anchor the C2 domain to the membrane. In short, the residue swap could negatively affect both protein folding and the stability of the SynGAP-membrane association.
c.1529T>G	I510S (3D Viewer)	GAP	Likely Pathogenic		1				-11.661	Likely Pathogenic	0.955	Likely Pathogenic	Ambiguous	0.926	Likely Pathogenic	4.00	Destabilizing	0.1	3.78	Destabilizing	3.89	Destabilizing	2.34	Destabilizing	-4.63	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	-1.44	Pathogenic	0.00	Affected	3.37	35	-1	-2	-5.3	-26.08	201.4	45.9	-0.4	0.2	0.0	0.3							X	Potentially Pathogenic	Ile510 is located in the middle of an α-helix (res. Gly502-Tyr518) within the inter-helix space of three helices (res. Gly502-Tyr518, Ala533-Val560, and res. Glu582-Met603). In the WT simulations, the sec-butyl side chain of Ile510 hydrophobically packs with other residues in the inter-helix space (e.g., Leu506, Leu610, Ile514, Ile602, Leu598). In the variant simulations, the hydroxyl group of Ser510 forms a hydrogen bond with the backbone atoms of Leu506 and Gly511 in the same α-helix, which could further weaken the α-helix integrity. This α-helix already shows weakness in the WT simulations due to Gly511. Although the simulations do not show large-scale effects, the residue swap could have a substantial impact due to the fundamental role of hydrophobic packing during protein folding.
c.703T>C	S235P (3D Viewer)	PH	Likely Pathogenic		1				-14.857	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.870	Likely Pathogenic	4.02	Destabilizing	0.1	6.91	Destabilizing	5.47	Destabilizing	1.23	Destabilizing	-4.24	Deleterious	0.917	Possibly Damaging	0.446	Benign	5.47	Benign	0.01	Affected	3.40	14	1	-1	-0.8	10.04	201.5	17.0	0.1	0.0	-0.6	0.0		X						Potentially Pathogenic	In the WT, the hydroxyl group of Ser235, located in a β-α loop between an anti-parallel β sheet strand (res. Gly227-Phe231) and an α helix (residues Ala236-Val250), forms hydrogen bonds with the GAP domain loop residue Glu680 and with the backbone amide groups of Ala237 and Glu238 from the α helix. In the variant simulations, the pyrrolidine ring of Pro235 cannot stabilize the α helix end or maintain tertiary bonding interactions between the PH and GAP domains via hydrogen bonding as effectively as serine.
c.1205T>G	L402R (3D Viewer)	C2	Likely Pathogenic		1				-13.800	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.522	Likely Pathogenic	4.10	Destabilizing	0.2	3.82	Destabilizing	3.96	Destabilizing	2.24	Destabilizing	-4.69	Deleterious	0.967	Probably Damaging	0.459	Possibly Damaging	3.69	Benign	0.00	Affected	3.38	28	-3	-2	-8.3	43.03	259.5	-55.4	0.0	0.0	1.4	0.0	X		X				X	Potentially Pathogenic	The iso-butyl side chain of Leu402, located in an anti-parallel β sheet strand (res. Ala399-Ile411), packs with residues inside the hydrophobic core of the C2 domain (e.g., Ile268, Ala404, Leu266, Val400). In the variant simulations, the positively charged guanidinium group of the Arg402 side chain is not suitable for the hydrophobic niche. Consequently, the side chain moves outward from the hydrophobic C2 domain core and stacks with the phenol ring of Tyr363 or forms H-bonds with the carboxamide group of the Gln361 side chain in the β sheet strand (res. Thr359-Tyr364). This movement induces extensive negative effects on the C2 domain structure.
c.1742G>C	R581P (3D Viewer)	GAP				6-33440794-G-C	1	6.20e-7	-13.309	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.562	Likely Pathogenic	4.13	Destabilizing	0.1	3.80	Destabilizing	3.97	Destabilizing	0.44	Likely Benign	-5.68	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.01	Pathogenic	0.07	Tolerated	3.37	34	-2	0	2.9	-59.07
c.1685C>A	P562Q (3D Viewer)	GAP				6-33440737-C-A			-15.705	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.778	Likely Pathogenic	4.18	Destabilizing	0.4	1.22	Ambiguous	2.70	Destabilizing	1.24	Destabilizing	-7.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	0.57	Pathogenic	0.00	Affected	3.37	35	-1	0	-1.9	31.01
c.1763T>A	L588H (3D Viewer)	GAP	Likely Pathogenic		1				-16.947	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.939	Likely Pathogenic	4.20	Destabilizing	0.2	3.69	Destabilizing	3.95	Destabilizing	2.26	Destabilizing	-6.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.42	Pathogenic	0.00	Affected	3.38	34	-2	-3	-7.0	23.98	214.3	20.9	0.0	0.0	0.0	0.2	X	X					X	Potentially Pathogenic	The isobutyl group of the Leu588 side chain, located in an α helix (res. Glu582-Met603), packs against hydrophobic residues in the inter-helix hydrophobic space (e.g., Ile584, Trp572, Phe484, Met470, Val473, Ile483).In the variant simulations, the imidazole ring of His588 is aromatic but contains polar delta and epsilon nitrogen atoms that are not suited for the hydrophobic niche. The protonated epsilon nitrogen forms a hydrogen bond with the backbone carbonyl group of Ala469, which can disrupt the continuity of the opposing α helix (res. Phe476-Lys460).While the residue swap could affect the tertiary assembly and the underlying protein folding process, it is difficult to determine if the mutation would be tolerated based solely on the variant simulations.
c.1172G>T	G391V (3D Viewer)	C2	Uncertain		1	6-33438077-G-T	3	1.86e-6	-6.642	Likely Benign	0.133	Likely Benign	Likely Benign	0.595	Likely Pathogenic	4.23	Destabilizing	1.3	4.81	Destabilizing	4.52	Destabilizing	-0.11	Likely Benign	-0.98	Neutral	0.994	Probably Damaging	0.887	Possibly Damaging	1.32	Pathogenic	0.10	Tolerated	3.69	8	-1	-3	4.6	42.08	228.6	-69.0	0.0	0.8	-0.5	0.3								Uncertain	Gly387 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. This loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play significant roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are visualized in the variant’s simulations, Val391 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. Since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1117G>A	G373R (3D Viewer)	C2				6-33438022-G-A	1	6.28e-7	-7.878	In-Between	0.652	Likely Pathogenic	Likely Benign	0.510	Likely Pathogenic	4.28	Destabilizing	3.5	0.14	Likely Benign	2.21	Destabilizing	0.21	Likely Benign	-0.64	Neutral	0.001	Benign	0.000	Benign	3.90	Benign	0.01	Affected	3.53	16	-2	-3	-4.1	99.14
c.1136C>G	S379W (3D Viewer)	C2	Uncertain		1	6-33438041-C-G			-8.898	Likely Pathogenic	0.388	Ambiguous	Likely Benign	0.520	Likely Pathogenic	4.32	Destabilizing	3.4	3.56	Destabilizing	3.94	Destabilizing	0.16	Likely Benign	-1.02	Neutral	0.998	Probably Damaging	0.844	Possibly Damaging	3.82	Benign	0.01	Affected	4.32	11	-2	-3	-0.1	99.14	271.3	-75.7	1.4	1.0	0.6	0.5								Uncertain	Ser379 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like tryptophan are rarely tolerated. Although no major negative structural effects are observed in the variant simulations, Trp379 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn
c.1123G>T	G375W (3D Viewer)	C2				6-33438028-G-T			-9.654	Likely Pathogenic	0.464	Ambiguous	Likely Benign	0.450	Likely Benign	4.33	Destabilizing	2.0	7.01	Destabilizing	5.67	Destabilizing	0.22	Likely Benign	-1.26	Neutral	0.992	Probably Damaging	0.869	Possibly Damaging	1.31	Pathogenic	0.01	Affected	4.32	12	-2	-7	-0.5	129.16
c.917T>A	V306D (3D Viewer)	C2	Uncertain		1				-18.289	Likely Pathogenic	0.986	Likely Pathogenic	Likely Pathogenic	0.530	Likely Pathogenic	4.40	Destabilizing	0.3	4.29	Destabilizing	4.35	Destabilizing	2.44	Destabilizing	-5.44	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.74	Pathogenic	0.00	Affected	3.38	19	-2	-3	-7.7	15.96	212.3	-18.3	-0.2	0.4	0.0	0.2	X		X				X	Potentially Pathogenic	The isopropyl group of Val396, located at the beginning of an anti-parallel β sheet strand (res. Thr305-Asn315), packs against multiple hydrophobic residues (e.g., Leu274, Trp308, Ala271) in the WT simulations. However, in the variant simulations, the negatively charged carboxylate group of the Asp306 side chain is not suitable for this hydrophobic niche. Consequently, the side chain moves out to interact with Ser300 in the β strand (res. Met289-Arg299) and the guanidinium group of Arg299 in the β hairpin loop.In the third simulation, the residue swap disrupts the C2 domain secondary structure and tertiary assembly to a large degree when the amino group of the Lys297 side chain rotates to form a salt bridge with Asp306. This drastic effect could potentially reflect the challenge presented by the residue swap during the C2 domain folding. Because the residue swap affects the C2 domain structure, the SynGAP-membrane association could also be impacted. However, this is beyond the scope of the solvent-only simulations to unravel.
c.1058T>C	L353P (3D Viewer)	C2	Uncertain		1				-7.913	In-Between	0.936	Likely Pathogenic	Ambiguous	0.464	Likely Benign	4.63	Destabilizing	0.1	10.19	Destabilizing	7.41	Destabilizing	2.17	Destabilizing	-3.70	Deleterious	0.947	Possibly Damaging	0.454	Possibly Damaging	1.29	Pathogenic	0.02	Affected	3.37	25	-3	-3	-5.4	-16.04
c.652T>A	F218I (3D Viewer)	PH				6-33435294-T-A	1	6.20e-7	-12.211	Likely Pathogenic	0.987	Likely Pathogenic	Likely Pathogenic	0.612	Likely Pathogenic	4.69	Destabilizing	0.2	5.93	Destabilizing	5.31	Destabilizing	1.18	Destabilizing	-3.81	Deleterious	0.510	Possibly Damaging	0.066	Benign	5.85	Benign	0.08	Tolerated	3.41	13	0	1	1.7	-34.02
c.1631G>C	R544P (3D Viewer)	GAP	Uncertain		2				-16.905	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.762	Likely Pathogenic	4.70	Destabilizing	0.1	4.19	Destabilizing	4.45	Destabilizing	1.14	Destabilizing	-4.88	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.48	Pathogenic	0.05	Affected	3.37	35	0	-2	2.9	-59.07	192.0	123.8	0.1	0.0	-0.3	0.0	X	X						Potentially Pathogenic	Arg544 is located in the middle of an α-helix (res. Ala533-Val560). In the WT simulations, the guanidinium side chain of Arg544 forms a salt bridge with the carboxylate groups of Glu548 on the same α-helix, and with Glu651 and Glu656 on an opposing α-helix (res. Glu666-Asp644). In the variant simulations, the pyrrolidine side chain of Pro544 cannot form any of the salt bridges that Arg544 does in the WT, potentially weakening the tertiary structure assembly. Additionally, Pro544 lacks the amide group, and thus, unlike Arg544 in the WT, is unable to form a hydrogen bond with the carbonyl of Gln540. This disruption breaks the continuity of the secondary structure element, causing the α-helix to bend slightly in the variant simulations. These negative structural effects could be more pronounced during protein folding and are likely to be undermined in the MD simulations.
c.1694T>G	L565R (3D Viewer)	GAP				6-33440746-T-G			-16.070	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.547	Likely Pathogenic	4.71	Destabilizing	0.1	1.88	Ambiguous	3.30	Destabilizing	2.66	Destabilizing	-5.97	Deleterious	0.999	Probably Damaging	0.998	Probably Damaging	2.74	Benign	0.00	Affected	3.37	35	-2	-3	-8.3	43.03
c.812C>A	A271D (3D Viewer)	C2	Pathogenic		1				-18.590	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.706	Likely Pathogenic	4.71	Destabilizing	0.4	2.67	Destabilizing	3.69	Destabilizing	1.59	Destabilizing	-5.52	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	0.62	Pathogenic	0.00	Affected	3.38	19	0	-2	-5.3	44.01	226.2	-63.4	0.0	0.0	0.9	0.1	X		X	X			X	Potentially Pathogenic	The methyl group of Ala271, located near the end of an anti-parallel β sheet strand (res. Arg259-Arg272), packs against multiple hydrophobic residues such as Val400, Val306, and Leu274 in the WT simulations. In the variant simulations, the carboxylate group of Asp271 is not suitable for the hydrophobic niche, causing the hydrophobic residues to make room for the swapped residue. Additionally, the carboxylate group of the Asp271 side chain forms hydrogen bonds with the backbone amide groups of Arg272 and Ala399 in the β sheet, or even forms a salt bridge with the amino group of the Lys394 side chain. This directly affects the integrity of the anti-parallel β sheet at the end. In short, the residue swap disrupts the C2 domain packing during folding, which could weaken the stability of the SynGAP-membrane association.
c.1714T>C	W572R (3D Viewer)	GAP							-17.511	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.894	Likely Pathogenic	4.84	Destabilizing	0.1	6.19	Destabilizing	5.52	Destabilizing	1.79	Destabilizing	-12.81	Deleterious					-1.25	Pathogenic	0.00	Affected	3.37	35	2	-3	3.6	30.03	312.6	-37.6	0.0	0.0	-1.0	0.0		X	X					Potentially Pathogenic	The indole ring of Trp572, located in an α-helix (res. Arg563-Glu578), lies in a hydrophobic inter-helix space, where it makes extensive hydrophobic interactions with nearby residues such as Met470, Phe569, Leu588, and Ile589. The guanidinium group of Arg572 is similarly sized to the tryptophan it replaced; however, it is also positively charged. In the variant simulations, Arg572 forms hydrogen bonds with other residues in the inter-helix space, such as Ser592 and the backbone carbonyl atom of Leu465. Additionally, Arg572 hydrophobically packs its carbon chain with surrounding residues such as Phe569 and Ile589.However, the introduced residue arginine is too hydrophilic and charged for the hydrophobic space, disrupting the hydrophobic packing of the inter-helix space. Indeed, in the second simulation, Arg572 successfully escapes the hydrophobic niche completely, causing the whole protein to partially unfold.Overall, the residue swap is highly likely to cause critical protein folding problems, as evidenced by the effects seen in the variant simulations.
c.2068T>C	S690P (3D Viewer)	GAP	Uncertain		1				-14.568	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.431	Likely Benign	4.84	Destabilizing	0.3	4.40	Destabilizing	4.62	Destabilizing	1.42	Destabilizing	-4.77	Deleterious	0.998	Probably Damaging	0.790	Possibly Damaging	3.44	Benign	0.01	Affected	3.42	17	1	-1	-0.8	10.04	207.5	15.1	0.1	0.0	-0.1	0.2	X	X						Potentially Pathogenic	The hydroxyl side chain of Ser690, located in an α-helix (res. Leu696-Leu685), forms a hydrogen bond with the backbone carbonyl group of Ser410 in an anti-parallel β-sheet of the C2 domain (res. Ile411-Ala399). In the variant simulations, the pyrrolidine side chain of Pro690 cannot form hydrogen bonds with the C2 domain residue, resulting in the loss of this inter-domain connection. Additionally, prolines lack a free amide group necessary for hydrogen bonding with the carbonyl group of Gly686, introducing a slight bend in the α-helix and compromising its integrity.
c.1145G>A	G382E (3D Viewer)	C2				6-33438050-G-A			-9.570	Likely Pathogenic	0.564	Ambiguous	Likely Benign	0.594	Likely Pathogenic	4.86	Destabilizing	1.7	6.64	Destabilizing	5.75	Destabilizing	0.48	Likely Benign	-0.96	Neutral	0.994	Probably Damaging	0.986	Probably Damaging	1.32	Pathogenic	0.03	Affected	4.32	9	-2	0	-3.1	72.06
c.1157G>T	G386V (3D Viewer)	C2				6-33438062-G-T			-6.405	Likely Benign	0.187	Likely Benign	Likely Benign	0.458	Likely Benign	4.88	Destabilizing	3.0	5.09	Destabilizing	4.99	Destabilizing	-0.17	Likely Benign	-0.64	Neutral	0.985	Probably Damaging	0.720	Possibly Damaging	3.91	Benign	0.01	Affected	4.32	3	-3	-1	4.6	42.08
c.1516C>T	L506F (3D Viewer)	GAP	Uncertain		1				-11.262	Likely Pathogenic	0.883	Likely Pathogenic	Ambiguous	0.464	Likely Benign	4.92	Destabilizing	0.8	5.76	Destabilizing	5.34	Destabilizing	0.91	Ambiguous	-3.98	Deleterious	0.999	Probably Damaging	0.997	Probably Damaging	1.62	Pathogenic	0.01	Affected	3.37	35	0	2	-1.0	34.02
c.1513T>G	Y505D (3D Viewer)	GAP	Likely Pathogenic		1				-14.078	Likely Pathogenic	0.993	Likely Pathogenic	Likely Pathogenic	0.718	Likely Pathogenic	4.98	Destabilizing	0.1	4.72	Destabilizing	4.85	Destabilizing	2.49	Destabilizing	-9.95	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.60	Benign	0.00	Affected	3.37	35	-3	-4	-2.2	-48.09
c.2071A>C	T691P (3D Viewer)	GAP	Likely Pathogenic		1				-13.801	Likely Pathogenic	0.905	Likely Pathogenic	Ambiguous	0.214	Likely Benign	5.04	Destabilizing	0.4	6.09	Destabilizing	5.57	Destabilizing	1.27	Destabilizing	-3.43	Deleterious	1.000	Probably Damaging	0.952	Probably Damaging	3.43	Benign	0.06	Tolerated	3.43	14	0	-1	-0.9	-3.99	188.9	33.0	0.1	0.0	-0.6	0.0	X	X						Potentially Pathogenic	The hydroxyl side chain of Thr691, located in an α-helix (res. Leu696-Leu685), can form hydrogen bonds with the backbone carbonyl and the side chain guanidinium group of Arg687. This interaction facilitates the simultaneous formation of salt bridges between Arg687 and Glu688 on the same α-helix. Additionally, Thr691 occasionally interacts with the thioether side chain of Met409 in an anti-parallel β-sheet of the C2 domain (res. Ile411-Ala399), although this interaction is not consistently maintained throughout the WT simulations. In the variant simulations, the pyrrolidine side chain of Pro691 lacks hydrogen bond donors, making a similar setup impossible. Moreover, proline lacks a free amide group necessary for hydrogen bonding with the carbonyl group of Arg687, introducing a slight bend in the α-helix and compromising its integrity.
c.1406C>A	A469D (3D Viewer)	GAP	Uncertain		1				-14.643	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.738	Likely Pathogenic	5.09	Destabilizing	0.2	4.16	Destabilizing	4.63	Destabilizing	1.68	Destabilizing	-3.48	Deleterious	0.999	Probably Damaging	0.996	Probably Damaging	-1.34	Pathogenic	0.21	Tolerated	3.37	34	0	-2	-5.3	44.01	237.0	-58.2	-0.2	0.1	0.8	0.1	X		X					Potentially Pathogenic	The methyl group of Ala469, located in an α helix (res. Ala461–Phe476), interacts with hydrophobic residues (e.g., Trp572, Leu588, Met470) in an inter-helix space formed by two other α helices (res. Glu582–Ser604, res. Arg563–Gly580). In the variant simulations, Asp469 introduces a negatively charged and bulky side chain into the hydrophobic niche. Consequently, the side chain of Asp469 rotates outward, allowing the carboxylate group to form a salt bridge with the guanidinium group of Arg575 on the protein surface. This interaction affects the continuity of the parent α helix (Ala461–Phe476). Due to the importance of hydrophobic packing, the structural effects could be more pronounced during actual protein folding.
c.1160G>T	G387V (3D Viewer)	C2	Uncertain		1	6-33438065-G-T	22	1.37e-5	-6.199	Likely Benign	0.153	Likely Benign	Likely Benign	0.390	Likely Benign	5.13	Destabilizing	1.8	6.44	Destabilizing	5.79	Destabilizing	-0.33	Likely Benign	-0.54	Neutral	0.069	Benign	0.077	Benign	1.32	Pathogenic	0.01	Affected	4.32	3	-1	-3	4.6	42.08	207.7	-68.4	-0.7	0.8	-0.5	0.1								Uncertain	Gly387 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. This loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play significant roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are visualized in the variant’s simulations, Val387 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. Since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1118G>T	G373V (3D Viewer)	C2	Uncertain		1	6-33438023-G-T	6	5.03e-6	-6.062	Likely Benign	0.112	Likely Benign	Likely Benign	0.428	Likely Benign	5.32	Destabilizing	3.2	0.82	Ambiguous	3.07	Destabilizing	0.09	Likely Benign	-0.98	Neutral	0.007	Benign	0.001	Benign	3.90	Benign	0.00	Affected	3.53	16	-1	-3	4.6	42.08	207.6	-68.1	1.9	1.1	-0.6	0.1								Uncertain	Gly373 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Val373 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on the Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1259T>C	F420S (3D Viewer)	GAP	Likely Pathogenic		1				-13.231	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.544	Likely Pathogenic	5.34	Destabilizing	0.1	5.73	Destabilizing	5.54	Destabilizing	2.14	Destabilizing	-7.43	Deleterious	0.998	Probably Damaging	0.938	Probably Damaging	3.09	Benign	0.00	Affected	3.37	29	-3	-2	-3.6	-60.10	213.3	57.8	0.0	0.0	-0.4	0.1							X	Potentially Pathogenic	In the WT, the phenyl ring of the Phe420 side chain, located on an α helix (res. Met414-Glu436), packs against hydrophobic residues in the interhelix area of the GAP domain (e.g., Leu689, Leu714, Leu717, Leu718). Although no large-scale adverse effects are seen in the variant simulations, the polar hydroxyl group of Ser420 is not suitable for the hydrophobic inter-helix space. Thus, the residue swap could affect protein folding. In theory, the introduced hydroxyl group could also lower the α helix integrity by H-bonding with the backbone atoms of neighboring residues in the same α helix. However, no such effect is seen in the variant simulations.
c.980T>C	L327P (3D Viewer)	C2	Pathogenic		2				-16.602	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.658	Likely Pathogenic	5.38	Destabilizing	0.1	4.00	Destabilizing	4.69	Destabilizing	2.62	Destabilizing	-5.97	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.52	Pathogenic	0.01	Affected	3.38	23	-3	-3	-5.4	-16.04	221.7	69.4	0.1	0.0	0.6	0.1	X							Potentially Pathogenic	The backbone amide group of Leu327, located in the middle of an anti-parallel β sheet strand (res. Ala322-Asp330), forms a hydrogen bond with the carbonyl group of Gly344 on a neighboring β strand (res. Lys336-Pro349) in the WT simulations. In contrast, in the variant simulations, the introduction of Pro327 destabilizes the hydrogen bonding between the two anti-parallel β strands because proline lacks the backbone amide group altogether. Additionally, in the WT simulations, the iso-butyl side chain of Leu327 packs against multiple hydrophobic residues (e.g., Leu274, V400, Val343), whereas the less bulky cyclic five-membered pyrrolidine ring of Pro327 cannot fill the same space as effectively. Thus, although no large-scale unfolding is observed during the variant simulations, the residue swap is likely to cause severe problems for the correct C2 domain folding, which could also affect the SynGAP-membrane association.	10.1016/j.ajhg.2020.11.011
c.922T>C	W308R (3D Viewer)	C2	Pathogenic		1				-12.264	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.868	Likely Pathogenic	5.40	Destabilizing	0.5	4.27	Destabilizing	4.84	Destabilizing	1.88	Destabilizing	-12.87	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	0.48	Pathogenic	0.00	Affected	3.38	19	2	-3	-3.6	-30.03	290.4	-26.7	-0.1	0.1	0.0	0.2	X		X				X	Potentially Pathogenic	The indole ring of Trp308, located in an anti-parallel β sheet strand (res. Thr305-Asn315), packs against multiple hydrophobic residues (e.g., Ile268, Val306, Cys282). The indole group of Trp308 also hydrogen bonds with the backbone atoms of the C2 domain residues forming the anti-parallel β sheet (e.g., Tyr280, Thr294). The guanidinium group of Arg308 is comparably sized to the tryptophan it replaced; however, it is also positively charged.In the variant simulations, the charged side chain remains buried deep in the hydrophobic part of the C2 domain, where it forms new hydrogen bonds with the backbone carbonyl atoms of surrounding residues (e.g., Val306, Ile268). However, the residue swap is likely to disrupt the hydrophobic packing during folding. At a minimum, the residue swap could affect the C2 domain stability and membrane association.
c.1517T>C	L506P (3D Viewer)	GAP	Likely Pathogenic		1				-12.088	Likely Pathogenic	0.998	Likely Pathogenic	Likely Pathogenic	0.737	Likely Pathogenic	5.48	Destabilizing	0.7	10.19	Destabilizing	7.84	Destabilizing	2.50	Destabilizing	-6.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	1.55	Pathogenic	0.00	Affected	3.37	35	-3	-3	-5.4	-16.04	182.6	64.9	0.1	0.0	0.2	0.1	X							Potentially Pathogenic	Leu506 is located in the middle of an α-helix (res. Gly502-Tyr518) within the inter-helix space of two helices (res. Gly502-Tyr518 and res. Glu582-Met603). In the WT simulations, the iso-butyl side chain of Leu506 hydrophobically packs with residues in the inter-helix space (e.g., Ile510, Phe597, Leu598, Ala601). In the variant simulations, the cyclic five-membered pyrrolidine ring of Pro506 is not as optimal as Leu506 for hydrophobic packing with nearby residues. Additionally, Pro506 cannot maintain the hydrogen bond with the backbone oxygen of Gly502 as Leu506 does in the WT, which disrupts the secondary structure element.
c.1163G>A	G388D (3D Viewer)	C2				6-33438068-G-A			-8.416	Likely Pathogenic	0.574	Likely Pathogenic	Likely Benign	0.618	Likely Pathogenic	5.56	Destabilizing	7.3	3.08	Destabilizing	4.32	Destabilizing	0.42	Likely Benign	-0.67	Neutral	0.994	Probably Damaging	0.986	Probably Damaging	1.32	Pathogenic	0.04	Affected	4.32	3	-1	1	-3.1	58.04
c.924G>C	W308C (3D Viewer)	C2	Pathogenic/Likely path.		2				-12.791	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.738	Likely Pathogenic	5.56	Destabilizing	0.3	4.38	Destabilizing	4.97	Destabilizing	1.26	Destabilizing	-11.95	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	0.48	Pathogenic	0.00	Affected	3.38	19	-8	-2	3.4	-83.07	230.8	60.5	-0.3	0.1	-0.4	0.4							X	Potentially Pathogenic	The indole ring of Trp308, located in an anti-parallel β sheet strand (res. Thr305-Asn315), packs against multiple hydrophobic residues (e.g., Ile268, Val306, Cys282). The indole group of Trp308 also hydrogen bonds with the backbone atoms of the C2 domain residues forming the anti-parallel β sheet (e.g., Tyr280, Thr294). The introduced Cys308 is smaller than the tryptophan it replaced. The thiol group of the Cys308 side chain is well-suited for the inner hydrophobic part of the C2 domain. Although the negative effects are essentially missing from the simulations, the side chain size difference between the residues is likely to disrupt the hydrophobic packing during folding. At a minimum, the residue swap could affect the C2 domain stability and membrane association.
c.1141G>A	G381R (3D Viewer)	C2				6-33438046-G-A			-8.990	Likely Pathogenic	0.652	Likely Pathogenic	Likely Benign	0.589	Likely Pathogenic	5.60	Destabilizing	0.9	2.80	Destabilizing	4.20	Destabilizing	0.20	Likely Benign	-0.82	Neutral	0.985	Probably Damaging	0.795	Possibly Damaging	1.32	Pathogenic	0.08	Tolerated	4.32	9	-2	-3	-4.1	99.14
c.1141G>C	G381R (3D Viewer)	C2				6-33438046-G-C	2	1.25e-6	-8.990	Likely Pathogenic	0.652	Likely Pathogenic	Likely Benign	0.589	Likely Pathogenic	5.60	Destabilizing	0.9	2.80	Destabilizing	4.20	Destabilizing	0.20	Likely Benign	-0.82	Neutral	0.985	Probably Damaging	0.795	Possibly Damaging	1.32	Pathogenic	0.08	Tolerated	4.32	9	-2	-3	-4.1	99.14
c.1763T>C	L588P (3D Viewer)	GAP	Uncertain		1				-14.771	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.932	Likely Pathogenic	5.61	Destabilizing	0.5	12.91	Destabilizing	9.26	Destabilizing	2.33	Destabilizing	-6.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.42	Pathogenic	0.00	Affected	3.38	34	-3	-3	-5.4	-16.04
c.1706T>C	F569S (3D Viewer)	GAP	Likely Pathogenic		2				-13.384	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.916	Likely Pathogenic	5.70	Destabilizing	0.1	5.38	Destabilizing	5.54	Destabilizing	2.45	Destabilizing	-7.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.32	Pathogenic	0.00	Affected	3.37	34	-3	-2	-3.6	-60.10	213.7	67.9	-0.1	0.0	-1.0	0.1							X	Potentially Pathogenic	Phe569 is located on an α-helix (res. Arg563-Glu578). In the WT simulations, the phenyl side chain of Phe569 packs with hydrophobic residues such as Trp572, Leu565, Ile589, Ile667, and Phe561, originating from three different α-helices (res. Ala533-Val560, res. Arg563-Glu578, and res. Ser641-Glu666). In the variant simulations, the acceptor/donor hydroxyl group of Ser569 forms hydrogen bonds with the carbonyl groups of Glu567 and Lys566 on the same α-helix, which could affect the α-helix integrity, although this is not observed in the simulations. While the simulations do not show large-scale effects, the residue swap could have a substantial impact on the protein structure due to the fundamental role of hydrophobic packing during protein folding.
c.1715G>C	W572S (3D Viewer)	GAP	Pathogenic		1				-17.461	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.775	Likely Pathogenic	5.78	Destabilizing	0.2	3.37	Destabilizing	4.58	Destabilizing	1.79	Destabilizing	-12.74	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.24	Pathogenic	0.01	Affected	3.37	35	-2	-3	0.1	-99.14	235.1	76.6	0.0	0.0	-0.4	0.1							X	Potentially Pathogenic	The introduced residue Ser572, located in an α-helix (res. Arg563-Glu578), is considerably smaller than the tryptophan it replaced. The indole ring of the Trp572 side chain lies in a hydrophobic inter-helix space, where it makes extensive hydrophobic interactions with nearby residues such as Met470, Phe569, Leu588, and Ile589. In the variant simulations, all these favorable packing interactions are completely removed, as the introduced residue Ser572 is too hydrophilic or small to fill the hydrophobic niche occupied by the indole ring. Moreover, the hydroxyl group of Ser572 forms hydrogen bonds with the carbonyl groups of Glu567 and Val568 within the same α-helix, potentially lowering its integrity. Overall, the residue swap is highly likely to cause critical protein folding problems that are underestimated based on the effects seen in the variant simulations.
c.1147G>T	G383W (3D Viewer)	C2	Uncertain		1	6-33438052-G-T	1	6.22e-7	-10.161	Likely Pathogenic	0.439	Ambiguous	Likely Benign	0.469	Likely Benign	5.81	Destabilizing	3.6	4.44	Destabilizing	5.13	Destabilizing	0.08	Likely Benign	-1.01	Neutral	0.959	Probably Damaging	0.704	Possibly Damaging	4.09	Benign	0.00	Affected	4.32	7	-2	-7	-0.5	129.16
c.851T>C	L284P	C2	Likely Pathogenic		1				-15.588	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.794	Likely Pathogenic	5.83	Destabilizing	0.2	5.81	Destabilizing	5.82	Destabilizing	1.89	Destabilizing	-6.17	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	1.64	Pathogenic	0.00	Affected			-3	-3	-5.4	-16.04
c.1499T>C	L500P (3D Viewer)	GAP	Uncertain		1				-15.898	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.894	Likely Pathogenic	5.91	Destabilizing	0.3	8.90	Destabilizing	7.41	Destabilizing	1.92	Destabilizing	-6.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.37	Pathogenic	0.01	Affected	3.37	35	-3	-3	-5.4	-16.04
c.1714T>G	W572G (3D Viewer)	GAP	Uncertain		1				-17.692	Likely Pathogenic	0.997	Likely Pathogenic	Likely Pathogenic	0.900	Likely Pathogenic	6.57	Destabilizing	0.2	7.57	Destabilizing	7.07	Destabilizing	1.83	Destabilizing	-11.98	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.24	Pathogenic	0.00	Affected	3.37	35	-7	-2	0.5	-129.16	195.2	127.9	0.0	0.0	-1.0	0.0							X	Potentially Pathogenic	The introduced residue Gly572, located in an α-helix (res. Arg563-Glu578), is considerably smaller than the tryptophan it replaced. The indole ring of the Trp572 side chain lies in a hydrophobic inter-helix space, where it makes extensive hydrophobic interactions with nearby residues such as Met470, Phe569, Leu588, and Ile589. In the variant simulations, all these favorable packing interactions are completely removed, as the introduced residue Gly572 essentially lacks a side chain altogether. Although not observed in the simulations, the residue swap could also weaken the integrity of the helix (res. Arg563-Glu578), as glycine is known as an “α-helix breaker.” Overall, the residue swap is highly likely to cause critical protein folding problems that are underestimated based on the effects seen in the variant simulations.
c.1163G>T	G388V (3D Viewer)	C2				6-33438068-G-T			-6.887	Likely Benign	0.120	Likely Benign	Likely Benign	0.620	Likely Pathogenic	6.58	Destabilizing	6.6	5.51	Destabilizing	6.05	Destabilizing	-0.11	Likely Benign	-0.93	Neutral	0.994	Probably Damaging	0.990	Probably Damaging	1.32	Pathogenic	0.01	Affected	4.32	3	-3	-1	4.6	42.08
c.1898T>C	L633P (3D Viewer)	GAP	Pathogenic/Likely path.		2				-15.669	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.693	Likely Pathogenic	6.60	Destabilizing	0.2	10.15	Destabilizing	8.38	Destabilizing	2.42	Destabilizing	-6.97	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.70	Benign	0.00	Affected	3.37	34	-3	-3	-5.4	-16.04	193.2	65.1	0.0	0.0	0.1	0.0	X							Potentially Pathogenic	The iso-butyl side chain of Leu633, located in the middle of an α helix (res. Glu617-Asn635), packs hydrophobically with nearby residues (e.g., Leu653, Val629, Leu551) in the WT simulations.In the variant simulations, the pyrrolidine side chain of Pro633 is not as optimal for hydrophobic packing as Leu633 in the WT. Additionally, proline lacks a free backbone amide group, so Pro633 cannot form a hydrogen bond with the backbone carbonyl group of Val629, which disrupts the continuity of the secondary structure element.
c.1652T>C	L551P (3D Viewer)	GAP	Likely Pathogenic		1				-14.620	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.953	Likely Pathogenic	6.66	Destabilizing	0.1	6.58	Destabilizing	6.62	Destabilizing	2.66	Destabilizing	-4.70	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-1.60	Pathogenic	0.01	Affected	3.37	35	-3	-3	-5.4	-16.04	208.6	60.9	0.1	0.0	-0.3	0.0	X							Potentially Pathogenic	L551 is located on an α-helix (res. Ala533-Val560). The iso-butyl side chain of Leu551 hydrophobically packs with nearby hydrophobic residues such as Cys547, Phe652, Leu633, and Ile630 in the inter-helix space. In the variant simulations, the pyrrolidine side chain of Pro551 is not as optimal as leucine for hydrophobic packing with the nearby residues. Moreover, Pro551 lacks the amide group, and thus, it cannot form a hydrogen bond with the backbone carbonyl group of Cys547, which disrupts the continuity of the secondary structure element.
c.2087T>C	L696P (3D Viewer)	GAP	Likely Pathogenic		1				-16.926	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.678	Likely Pathogenic	6.66	Destabilizing	0.2	10.84	Destabilizing	8.75	Destabilizing	2.13	Destabilizing	-6.58	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	3.00	Benign	0.00	Affected	3.46	13	-3	-3	-5.4	-16.04	180.6	65.9	0.1	0.0	-0.6	0.1	X							Potentially Pathogenic	The isobutyl side chain of Leu696, located in the middle of an α-helix (res. Leu685-Gln702), engages in hydrophobic packing with nearby residues (e.g., Leu441, Leu431, Leu692, Leu714) in the inter-helix space. Prolines lack a free amide group necessary for hydrogen bonding with the carbonyl group of Leu692 in the same manner as Leu696 in the WT. Consequently, the residue swap with proline disrupts the continuity of the secondary structure element in the variant simulations. Additionally, the side chain of Pro696 is not as optimal as Leu696 for hydrophobic packing in the inter-helix space.
c.1802C>A	A601E (3D Viewer)	GAP	Conflicting		2				-16.752	Likely Pathogenic	0.992	Likely Pathogenic	Likely Pathogenic	0.588	Likely Pathogenic	6.68	Destabilizing	0.8	5.76	Destabilizing	6.22	Destabilizing	1.24	Destabilizing	-4.98	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	2.54	Benign	0.00	Affected	3.37	35	0	-1	-5.3	58.04	240.0	-82.3	0.0	0.0	0.7	0.1		X	X				X	Potentially Pathogenic	The methyl side chain of Ala601, located on an α helix (res. Glu582-Met603), packs hydrophobically against other hydrophobic residues in the inter-helix space (e.g., Phe597, Leu598, Leu506, Phe608).In the variant simulations, the carboxylate group of Glu601 faces the inter-helix space and is forced to shift slightly away from the hydrophobic niche. Additionally, in two of the simulations, Glu601 forms a salt bridge with Arg499, causing the otherwise stable salt bridge between Arg499 and Glu496 at the outer surface of an α helix (res. Leu489-Glu519) to break due to the residue swap.These effects suggest that the protein folding process could be seriously affected. Moreover, due to its location at the GAP-Ras interface, it could also impact the complex formation with the GTPase.
c.1481T>G	I494R (3D Viewer)	GAP	Likely Pathogenic		1				-15.758	Likely Pathogenic	0.995	Likely Pathogenic	Likely Pathogenic	0.911	Likely Pathogenic	6.71	Destabilizing	0.3	3.40	Destabilizing	5.06	Destabilizing	2.19	Destabilizing	-6.43	Deleterious	0.999	Probably Damaging	0.957	Probably Damaging	-1.41	Pathogenic	0.00	Affected	3.37	35	-2	-3	-9.0	43.03	273.9	-59.8	0.0	0.0	0.0	0.1	X	X	X				X	Potentially Pathogenic	The sec-butyl side chain of Ile494, located in an α-helix (res. Leu489-Glu519), packs against hydrophobic residues (e.g., Phe484, Leu465, Trp572, Ala493, Met468) in an inter-helix space (res. Leu489-Glu519 and res. Ala461-Phe476). In the variant simulations, the bulkier and positively charged residue, Arg494, weakens the integrity of the opposing helix. Additionally, the bulkier Arg494 stacks with Phe484, causing the α-helices to move farther apart to accommodate it. This mutation could have substantial negative effects due to the fundamental role of hydrophobic packing, which is disrupted by Arg494 during protein folding.
c.1292T>C	L431P (3D Viewer)	GAP	Likely Pathogenic		1				-14.222	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.659	Likely Pathogenic	6.78	Destabilizing	0.3	11.59	Destabilizing	9.19	Destabilizing	2.29	Destabilizing	-6.39	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	2.91	Benign	0.05	Affected	3.37	29	-3	-3	-5.4	-16.04	222.4	62.8	0.1	0.0	0.1	0.0	X							Potentially Pathogenic	The iso-butyl side chain of Leu431, located in an α helix (res. Met414-Glu436), packs against other hydrophobic residues in an interhelix space (e.g., Val434, Leu435, Leu696, Leu711) in the WT simulations. While the backbone amide group of Leu431 forms an H-bond with the carbonyl group of His427, the cyclic five-membered pyrrolidine ring of Pro431, lacking the necessary amide group, cannot do the same. Thus, although the cyclic five-membered pyrrolidine ring of Pro431 packs almost as favorably as the side chain of Leu431 in the hydrophobic niche, the residue swap causes the α helix to partially unfold in the variant simulations.
c.1352T>C	L451P (3D Viewer)	GAP	Likely Pathogenic		1				-14.549	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.750	Likely Pathogenic	6.92	Destabilizing	0.2	8.57	Destabilizing	7.75	Destabilizing	2.58	Destabilizing	-6.81	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.43	Pathogenic	0.00	Affected	3.37	34	-3	-3	-5.4	-16.04
c.1142G>T	G381V (3D Viewer)	C2	Uncertain		1	6-33438047-G-T	2	1.25e-6	-5.967	Likely Benign	0.146	Likely Benign	Likely Benign	0.618	Likely Pathogenic	7.16	Destabilizing	1.0	4.10	Destabilizing	5.63	Destabilizing	-0.32	Likely Benign	-0.95	Neutral	0.386	Benign	0.157	Benign	1.32	Pathogenic	0.10	Tolerated	4.32	9	-1	-3	4.6	42.08	214.6	-68.8	0.3	0.7	-0.5	0.3								Uncertain	Gly381 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Val381 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effects on Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1394T>C	L465P (3D Viewer)	GAP	Likely Pathogenic		1				-14.824	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.778	Likely Pathogenic	7.18	Destabilizing	0.3	10.85	Destabilizing	9.02	Destabilizing	2.73	Destabilizing	-6.96	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	2.29	Pathogenic	0.00	Affected	3.37	34	-3	-3	-5.4	-16.04	211.1	65.9	0.1	0.0	-0.2	0.0	X							Potentially Pathogenic	The iso-butyl side chain of Leu465, located in the middle of an α helix (res. Ala461–Phe476), packs with hydrophobic residues (e.g., Phe464, Met468, Tyr497, Ile494) in an inter-helix space formed with two other α helices (res. Ala461–Phe476 and res. Thr488-Gly502). In the variant simulations, the cyclic five-membered pyrrolidine ring of Pro465 is not as optimal as the side chain of Leu465 for filling the three α helix hydrophobic niche. Although the residue swap does not cause a large-scale conformational shift during the simulations, the H-bond between the backbone amide group of Leu465 and the backbone carbonyl group of Ala461 is lost. This, in turn, breaks the continuity of the α helix secondary structure element.
c.1726T>C	C576R (3D Viewer)	GAP	Conflicting		2				-14.886	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.579	Likely Pathogenic	7.20	Destabilizing	1.0	4.09	Destabilizing	5.65	Destabilizing	1.64	Destabilizing	-10.88	Deleterious	0.999	Probably Damaging	0.996	Probably Damaging	3.38	Benign	0.00	Affected	3.37	35	-3	-4	-7.0	53.05
c.1639T>C	C547R (3D Viewer)	GAP	Uncertain		1				-16.967	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.900	Likely Pathogenic	7.76	Destabilizing	0.8	5.83	Destabilizing	6.80	Destabilizing	1.69	Destabilizing	-11.60	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	-1.33	Pathogenic	0.02	Affected	3.37	35	-4	-3	-7.0	53.05	267.4	-90.3	0.0	0.0	-0.1	0.1	X	X	X				X	Potentially Pathogenic	Cys547 is located in an α-helix (res. Ala533-Val560). The thiol side chain of Cys is situated in a hydrophobic inter-helix space, where it packs hydrophobically with other residues such as Ile626, Leu551, and Phe652. Additionally, the thiol side chain of Cys547 weakly hydrogen bonds with the carbonyl group of Leu543 in the same α-helix. In the variant simulations, the bulkier, positively charged guanidinium group of Arg547 must rotate out of the hydrophobic space. Consequently, it forms ionic interactions with the carboxylate groups of Glu548 in the same helix and Glu656 in the neighboring α-helix (res. Glu666-Asp644). This causes the two helices to slightly separate, significantly affecting the secondary structure integrity of the latter helix. These negative structural effects could be more pronounced during protein folding and are likely to be undermined in the MD simulations.
c.1640G>A	C547Y (3D Viewer)	GAP	Pathogenic		1				-15.871	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.874	Likely Pathogenic	8.53	Destabilizing	1.8	6.20	Destabilizing	7.37	Destabilizing	0.62	Ambiguous	-10.57	Deleterious	1.000	Probably Damaging	0.998	Probably Damaging	-1.33	Pathogenic	0.06	Tolerated	3.37	35	0	-2	-3.8	60.04	280.1	-54.8	0.0	0.0	0.0	0.0		X	X				X	Potentially Pathogenic	Cys547 is located in an α-helix (res. Ala533-Val560). The thiol side chain of Cys547 is situated in a hydrophobic inter-helix space, where it packs hydrophobically with other residues such as Ile626, Leu551, and Phe652. Additionally, the thiol side chain of Cys weakly hydrogen bonds with the carbonyl group of Leu543 in the same α-helix. In the variant simulations, the bulkier phenol ring of Tyr547, with its polar hydroxyl group, is less suited for the hydrophobic space. Consequently, it moves outside and forms a hydrogen bond with the carbonyl group of Phe652 in the neighboring α-helix (res. Glu666-Asp644). This causes the two helices to slightly separate, negatively affecting the secondary structure integrity of the latter helix. These negative structural effects could be more pronounced during protein folding and are likely to be undermined in the MD simulations.
c.1814C>G	P605R (3D Viewer)	GAP	Uncertain		1				-13.745	Likely Pathogenic	0.996	Likely Pathogenic	Likely Pathogenic	0.845	Likely Pathogenic	8.71	Destabilizing	2.5	6.46	Destabilizing	7.59	Destabilizing	0.92	Ambiguous	-8.95	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	0.69	Pathogenic	0.00	Affected	3.37	35	0	-2	-2.9	59.07	281.7	-118.1	-0.2	0.0	0.5	0.1		X	X	X			X	Potentially Pathogenic	Pro605 is located in a short turn between an α helix (res. Glu582-Met603) and a short α helical section (res. Ser606-Phe608). The pyrrolidine side chain of Pro605 packs hydrophobically with nearby hydrophobic residues (e.g., Ile514, Leu623, Leu610) in the inter-helix space. Additionally, proline lacks a free backbone amide group, which breaks the α helix and facilitates the turn in the WT structure.In the variant simulations, the guanidinium side chain of Arg605 is bulkier than proline, and its positively charged guanidinium group faces mostly hydrophobic residues (e.g., Ile514, Leu623, Leu610). As a result, it needs to rotate away from the hydrophobic niche. The residue swap could have a more profound effect on the actual folding process, for example, by preventing the bending at the α helix end.Moreover, due to its location at the GAP-Ras interface, the residue swap could affect the GAP-Ras association.
c.1141G>T	G381W (3D Viewer)	C2				6-33438046-G-T	1	6.24e-7	-10.173	Likely Pathogenic	0.438	Ambiguous	Likely Benign	0.576	Likely Pathogenic	8.81	Destabilizing	2.0	3.17	Destabilizing	5.99	Destabilizing	0.02	Likely Benign	-1.04	Neutral	0.996	Probably Damaging	0.920	Probably Damaging	1.31	Pathogenic	0.01	Affected	4.32	9	-2	-7	-0.5	129.16
c.1030G>A	G344S (3D Viewer)	C2	Pathogenic		5				-11.254	Likely Pathogenic	0.986	Likely Pathogenic	Likely Pathogenic	0.790	Likely Pathogenic	9.02	Destabilizing	0.7	6.08	Destabilizing	7.55	Destabilizing	0.98	Ambiguous	-5.28	Deleterious	1.000	Probably Damaging	1.000	Probably Damaging	-0.45	Pathogenic	0.04	Affected	3.37	25	1	0	-0.4	30.03	217.3	-51.7	0.0	0.1	0.2	0.1			X				X	Potentially Pathogenic	Because Gly344 lacks a proper side chain, it allows the anti-parallel β sheet strand (res. Gly341-Pro349) to have a slight twist. Within a β strand, side chains normally alternate between outward and inward positions, but glycine is an exception as it allows the alternating pattern to skip a residue. Introducing serine or any other residue with a side chain at position 344 prevents this unique skip in the alternating pattern, causing structural strain or likely preventing correct folding altogether. Additionally, Tyr342 shields Gly344 from the solvent, contributing to twist formation in the β sheet and stabilizing the β-strand.In the variant simulations, the side chain of Ser344 assumes the inward position. However, the hydrophobic niche formed by multiple C2 domain residues (e.g., Val365, Val343, Leu327) is not accommodating for its hydroxyl group. The outward position, not seen in the simulations, would be equally disadvantageous due to the presence of hydrophobic residues on that side as well (e.g., Leu345, Tyr342). Serine is also not well-suited for twist formation, as it tends to suppress twisting and bending in β sheets. At this position, the hydroxyl group of Ser344 could also form hydrogen bonds with the backbone atoms of the Gly-rich Ω loop in the C2 domain (e.g., Thr366, Leu367, Gly378; res. Pro364-Pro398), potentially adversely affecting membrane-loop dynamics and ultimately compromising the stability of the SynGAP-membrane association.
c.2075T>C	L692P (3D Viewer)	GAP	Uncertain		1				-16.447	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.668	Likely Pathogenic	9.19	Destabilizing	0.1	13.20	Destabilizing	11.20	Destabilizing	1.69	Destabilizing	-6.98	Deleterious	1.000	Probably Damaging	0.999	Probably Damaging	3.06	Benign	0.00	Affected	3.42	17	-3	-3	-5.4	-16.04	186.2	62.8	-0.2	0.1	-0.7	0.3	X							Potentially Pathogenic	The isobutyl side chain of Leu692, located in the middle of an α-helix (res. Leu685-Gln702), engages in hydrophobic packing with nearby residues (e.g., Leu441, Leu431, Leu696) in the inter-helix space. Prolines lack a free amide group necessary for hydrogen bonding with the carbonyl group of Glu688 in the same manner as Leu692 in the WT. Consequently, the residue swap with proline disrupts the continuity of the secondary structure element in the variant simulations. Additionally, the side chain of Pro692 is not as optimal as Leu692 for hydrophobic packing in the inter-helix space.
c.1354G>T	V452F (3D Viewer)	GAP	Uncertain		1				-14.769	Likely Pathogenic	0.975	Likely Pathogenic	Likely Pathogenic	0.511	Likely Pathogenic	9.21	Destabilizing	0.1	0.37	Likely Benign	4.79	Destabilizing	0.61	Ambiguous	-4.94	Deleterious	0.999	Probably Damaging	0.993	Probably Damaging	3.29	Benign	0.00	Affected	3.37	34	-1	-1	-1.4	48.04	249.4	-35.7	0.0	0.0	0.4	0.1							X	Potentially Pathogenic	The iso-propyl side chain of Val452, located in the middle of an α helix (res. Val441-Ser457), packs against hydrophobic residues in the inter-helix space at the intersection of three α helices (e.g., Leu500, His453, Leu465). In the variant simulations, the larger side chain of Phe452 cannot pack against the opposing α helix (res. Leu489-Glu519) as efficiently as valine. Due to space restrictions, the phenol ring adjusts to make room by rotating slightly sideways in the inter-helix space. Besides this small and local shift, no large-scale effects on the protein structure are seen based on the simulations. However, the size difference between the swapped residues could affect the protein folding process.
c.1133G>A	G378D (3D Viewer)	C2				6-33438038-G-A	1	6.97e-7	-7.767	In-Between	0.576	Likely Pathogenic	Likely Benign	0.619	Likely Pathogenic	11.41	Destabilizing	5.0	11.84	Destabilizing	11.63	Destabilizing	0.50	Likely Benign	-0.63	Neutral	1.000	Probably Damaging	0.992	Probably Damaging	1.32	Pathogenic	0.08	Tolerated	4.32	12	-1	1	-3.1	58.04
c.1133G>T	G378V (3D Viewer)	C2				6-33438038-G-T	1	6.97e-7	-6.837	Likely Benign	0.168	Likely Benign	Likely Benign	0.606	Likely Pathogenic	12.88	Destabilizing	5.0	21.64	Destabilizing	17.26	Destabilizing	0.04	Likely Benign	-0.98	Neutral	1.000	Probably Damaging	0.994	Probably Damaging	1.32	Pathogenic	0.04	Affected	4.32	12	-3	-1	4.6	42.08
c.698G>A	C233Y (3D Viewer)	PH							-17.893	Likely Pathogenic	1.000	Likely Pathogenic	Likely Pathogenic	0.904	Likely Pathogenic	13.15	Destabilizing	4.6	0.04	Likely Benign	6.60	Destabilizing	0.71	Ambiguous	-9.79	Deleterious	0.940	Possibly Damaging	0.459	Possibly Damaging	5.71	Benign	0.00	Affected	4.29	391	0	-2	-3.8	60.04	248.9	-63.0	0.0	0.3	0.0	0.4	X						X	Potentially Pathogenic	The introduced residue Tyr233 is located in a β-α loop between an anti-parallel β sheet strand (res. Gly227-Ala232) and an α helix (residues Ala236-Val250). Although the thiol group of a cysteine side chain is not a strong hydrogen bond acceptor or donor, it facilitates hydrogen bonding between Cys233 and the backbone carbonyl of Ala232 in the WT simulations. In the variant simulations, the bulky phenol ring of the Tyr233 side chain stacks with the indole ring of the Trp242 side chain. This interaction could alter the tertiary assembly of the β sheet and α helix due to the residue swap. Indeed, in the second replica simulation, the protein structure begins to unfold to accommodate the introduced Tyr233 side chain.	10.1016/j.ajhg.2020.11.011
c.2003C>T	S668F (3D Viewer)	GAP	Likely Pathogenic		1				-15.047	Likely Pathogenic	0.999	Likely Pathogenic	Likely Pathogenic	0.643	Likely Pathogenic	16.72	Destabilizing	5.0	11.07	Destabilizing	13.90	Destabilizing	0.00	Likely Benign	-5.98	Deleterious	0.999	Probably Damaging	0.935	Probably Damaging	3.18	Benign	0.00	Affected	3.38	28	-3	-2	3.6	60.10	250.9	-59.6	-0.1	0.1	0.0	0.1		X	X				X	Potentially Pathogenic	In the WT simulations, the hydroxyl side chain of Ser668, located on an α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), forms hydrogen bonds with the backbone carbonyl groups of Leu664, Tyr665, and Glu666, as well as the guanidinium group of Arg573 on a nearby α-helix (res. Arg563-Glu578). In the variant simulations, the side chain of Phe668 cannot maintain the same hydrogen-bond network. Due to its larger size, it moves away to avoid steric hindrance. In the WT simulations, a network of hydrogen bonds between several residues (e.g., Asn669, Lys566, and Glu666) keeps both α-helices and the proceeding loop (res. Asn669-Asp684) tightly connected, but this setup is not present in the variant simulations. Additionally, in the variant simulations, the side chain of Arg573 shifts to form a more stable salt bridge with the carboxylate group of Glu582 instead of hydrogen bonding with Ser668 as in the WT simulations.