SynGap Missense Server

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

c.dna Variant SGM Consensus 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.1490A>GY497C
(3D Viewer)
Likely PathogenicGAPUncertain 1-11.872Likely Pathogenic0.948Likely PathogenicAmbiguous0.806Likely Pathogenic3.88Destabilizing0.14.76Destabilizing4.32Destabilizing1.40Destabilizing-8.82Deleterious1.000Probably Damaging0.995Probably Damaging-1.65Pathogenic0.03Affected3.37350-23.8-60.04209.959.1-0.10.0-0.30.1XXPotentially PathogenicTyr497 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.2158G>AD720N
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33441623-G-A53.10e-6-9.135Likely Pathogenic0.654Likely PathogenicLikely Benign0.289Likely Benign0.01Likely Benign0.0-0.20Likely Benign-0.10Likely Benign0.46Likely Benign-3.74Deleterious1.000Probably Damaging0.995Probably Damaging2.18Pathogenic0.01Affected3.509120.0-0.98
c.1718G>AR573Q
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-9.900Likely Pathogenic0.923Likely PathogenicAmbiguous0.733Likely Pathogenic2.28Destabilizing0.81.94Ambiguous2.11Destabilizing1.08Destabilizing-3.16Deleterious1.000Probably Damaging0.995Probably Damaging-1.31Pathogenic0.12Tolerated3.3735111.0-28.06230.149.90.00.0-0.60.0XXPotentially PathogenicThe 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.1742G>AR581Q
(3D Viewer)
Likely PathogenicGAPBenign 16-33440794-G-A84.96e-6-7.584In-Between0.673Likely PathogenicLikely Benign0.481Likely Benign1.31Ambiguous0.1-0.42Likely Benign0.45Likely Benign0.88Ambiguous-2.77Deleterious1.000Probably Damaging0.995Probably Damaging-1.21Pathogenic0.11Tolerated3.3734111.0-28.06239.653.5-0.20.2-0.40.1XPotentially PathogenicArg581 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.2435C>AP812HSH3-binding motifUncertain 26-33442987-C-A31.86e-6-7.470In-Between0.698Likely PathogenicLikely Benign0.272Likely Benign-2.81Deleterious1.000Probably Damaging0.995Probably Damaging2.68Benign0.00Affected4.3240-2-1.640.02
c.2514C>AN838KLikely PathogenicUncertain 2-8.470Likely Pathogenic0.862Likely PathogenicAmbiguous0.097Likely Benign-2.78Deleterious0.997Probably Damaging0.995Probably Damaging2.69Benign0.16Tolerated3.77510-0.414.07
c.2619C>GS873RUncertain 16-33443171-C-G16.20e-7-5.856Likely Benign0.976Likely PathogenicLikely Pathogenic0.192Likely Benign-2.74Deleterious0.997Probably Damaging0.995Probably Damaging2.67Benign0.06Tolerated3.7750-1-3.769.11
c.2724G>CQ908HLikely BenignConflicting 46-33443276-G-C16.20e-7-4.658Likely Benign0.311Likely BenignLikely Benign0.112Likely Benign-0.74Neutral0.996Probably Damaging0.995Probably Damaging2.58Benign0.05Affected3.775300.39.01
c.3374G>CG1125ALikely BenignUncertain 16-33443926-G-C16.68e-7-6.569Likely Benign0.083Likely BenignLikely Benign0.232Likely Benign-0.60Neutral0.999Probably Damaging0.995Probably Damaging4.60Benign0.11Tolerated3.775102.214.03
c.3595G>AE1199KCoiled-coilUncertain 16-33446587-G-A16.20e-7-10.853Likely Pathogenic0.954Likely PathogenicAmbiguous0.171Likely Benign-2.26Neutral1.000Probably Damaging0.995Probably Damaging2.52Benign0.00Affected3.77501-0.4-0.94
c.3686A>CQ1229PLikely PathogenicCoiled-coilUncertain 1-10.397Likely Pathogenic0.980Likely PathogenicLikely Pathogenic0.422Likely Benign-3.69Deleterious0.998Probably Damaging0.995Probably Damaging1.75Pathogenic0.12Tolerated3.7750-11.9-31.01
c.3806T>AV1269ELikely PathogenicCoiled-coilUncertain 1-11.418Likely Pathogenic0.989Likely PathogenicLikely Pathogenic0.403Likely Benign-5.05Deleterious0.999Probably Damaging0.995Probably Damaging2.09Pathogenic0.00Affected3.775-2-2-7.729.98
c.3821G>AR1274HLikely Benign 16-33447869-G-A42.58e-6-5.259Likely Benign0.256Likely BenignLikely Benign0.149Likely Benign-3.20Deleterious1.000Probably Damaging0.995Probably Damaging2.49Pathogenic0.01Affected3.775021.3-19.05
c.451G>CD151HLikely PathogenicUncertain 16-33432748-G-C21.26e-6-11.747Likely Pathogenic0.994Likely PathogenicLikely Pathogenic0.335Likely Benign-3.90Deleterious0.999Probably Damaging0.995Probably Damaging3.86Benign0.00Affected3.615-110.322.05
c.937G>AE313K
(3D Viewer)
Likely PathogenicC2Likely Benign 1-12.902Likely Pathogenic0.959Likely PathogenicLikely Pathogenic0.575Likely Pathogenic0.64Ambiguous0.61.40Ambiguous1.02Ambiguous0.75Ambiguous-3.31Deleterious1.000Probably Damaging0.995Probably Damaging1.90Pathogenic0.02Affected01-0.4-0.94
c.928G>AE310K
(3D Viewer)
Likely PathogenicC2Conflicting 4-14.601Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.764Likely Pathogenic1.97Ambiguous1.23.66Destabilizing2.82Destabilizing1.02Destabilizing-3.68Deleterious1.000Probably Damaging0.995Probably Damaging1.19Pathogenic0.01Affected3.381901-0.4-0.94213.458.00.10.00.20.1XPotentially PathogenicThe 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.1045C>TP349S
(3D Viewer)
C2Uncertain 1-7.654In-Between0.217Likely BenignLikely Benign0.277Likely Benign1.92Ambiguous0.12.28Destabilizing2.10Destabilizing0.87Ambiguous-6.13Deleterious1.000Probably Damaging0.996Probably Damaging1.66Pathogenic0.06Tolerated3.37251-10.8-10.04194.9-18.1-0.10.00.20.1XXPotentially PathogenicThe 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.1084T>CW362R
(3D Viewer)
Likely PathogenicC2Pathogenic 2-14.004Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.706Likely Pathogenic2.64Destabilizing0.33.90Destabilizing3.27Destabilizing1.10Destabilizing-12.87Deleterious0.999Probably Damaging0.996Probably Damaging1.28Pathogenic0.00Affected3.39242-3-3.6-30.03287.5-34.1-0.20.1-0.60.2XXXPotentially PathogenicThe 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.1559C>TS520F
(3D Viewer)
Likely PathogenicGAPUncertain 1-12.541Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.833Likely Pathogenic-1.20Ambiguous0.40.39Likely Benign-0.41Likely Benign0.25Likely Benign-5.57Deleterious0.999Probably Damaging0.996Probably Damaging-1.36Pathogenic0.00Affected3.3735-2-33.660.10
c.1390T>GF464V
(3D Viewer)
Likely PathogenicGAPUncertain 1-12.254Likely Pathogenic0.994Likely PathogenicLikely Pathogenic0.592Likely Pathogenic3.61Destabilizing0.12.89Destabilizing3.25Destabilizing1.40Destabilizing-6.96Deleterious0.998Probably Damaging0.996Probably Damaging3.36Benign0.04Affected3.3734-1-11.4-48.04210.140.5-0.10.0-0.90.3XPotentially PathogenicThe 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.1406C>AA469D
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.643Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.738Likely Pathogenic5.09Destabilizing0.24.16Destabilizing4.63Destabilizing1.68Destabilizing-3.48Deleterious0.999Probably Damaging0.996Probably Damaging-1.34Pathogenic0.21Tolerated3.37340-2-5.344.01237.0-58.2-0.20.10.80.1XXPotentially PathogenicThe 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.1712C>TS571L
(3D Viewer)
Likely PathogenicGAPUncertain 16-33440764-C-T16.23e-7-11.651Likely Pathogenic0.660Likely PathogenicLikely Benign0.841Likely Pathogenic-1.53Ambiguous0.1-1.05Ambiguous-1.29Ambiguous0.27Likely Benign-5.61Deleterious1.000Probably Damaging0.996Probably Damaging-1.25Pathogenic0.04Affected3.3735-2-34.626.08
c.1726T>CC576R
(3D Viewer)
Likely PathogenicGAPConflicting 2-14.886Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.579Likely Pathogenic7.20Destabilizing1.04.09Destabilizing5.65Destabilizing1.64Destabilizing-10.88Deleterious0.999Probably Damaging0.996Probably Damaging3.38Benign0.00Affected3.3735-3-4-7.053.05
c.1991T>CL664S
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33441250-T-C16.20e-7-16.498Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.543Likely Pathogenic3.75Destabilizing0.23.63Destabilizing3.69Destabilizing2.77Destabilizing-5.99Deleterious1.000Probably Damaging0.996Probably Damaging2.85Benign0.00Affected3.3828-3-2-4.6-26.08215.550.10.00.0-0.20.2XPotentially BenignThe 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.3009C>GS1003RUncertain 1-5.113Likely Benign0.991Likely PathogenicLikely Pathogenic0.141Likely Benign-1.88Neutral0.999Probably Damaging0.996Probably Damaging2.48Pathogenic0.00Affected3.7750-1-3.769.11
c.3253C>TR1085WUncertain 16-33443805-C-T21.26e-6-6.339Likely Benign0.821Likely PathogenicAmbiguous0.202Likely Benign-3.15Deleterious1.000Probably Damaging0.996Probably Damaging2.70Benign0.00Affected3.775-323.630.03
c.3413C>AS1138YUncertain 16-33444448-C-A31.86e-6-6.610Likely Benign0.449AmbiguousLikely Benign0.391Likely Benign-2.51Deleterious0.997Probably Damaging0.996Probably Damaging5.41Benign0.05Affected4.324-2-3-0.576.10
c.3820C>TR1274CUncertain 16-33447868-C-T-6.467Likely Benign0.439AmbiguousLikely Benign0.170Likely Benign-5.22Deleterious1.000Probably Damaging0.996Probably Damaging2.46Pathogenic0.00Affected3.775-4-37.0-53.05
c.929A>GE310G
(3D Viewer)
Likely PathogenicC2Pathogenic 1-14.132Likely Pathogenic0.995Likely PathogenicLikely Pathogenic0.848Likely Pathogenic2.38Destabilizing0.73.56Destabilizing2.97Destabilizing0.36Likely Benign-6.43Deleterious1.000Probably Damaging0.996Probably Damaging1.12Pathogenic0.00Affected3.3819-203.1-72.06
c.1256A>GE419G
(3D Viewer)
Likely PathogenicGAPUncertain 1-10.589Likely Pathogenic0.956Likely PathogenicLikely Pathogenic0.469Likely Benign1.41Ambiguous0.01.94Ambiguous1.68Ambiguous0.83Ambiguous-6.42Deleterious1.000Probably Damaging0.997Probably Damaging3.31Benign0.02Affected3.37290-23.1-72.06165.3110.80.00.0-0.10.0XPotentially PathogenicThe 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.1516C>TL506F
(3D Viewer)
Likely PathogenicGAPUncertain 1-11.262Likely Pathogenic0.883Likely PathogenicAmbiguous0.464Likely Benign4.92Destabilizing0.85.76Destabilizing5.34Destabilizing0.91Ambiguous-3.98Deleterious0.999Probably Damaging0.997Probably Damaging1.62Pathogenic0.01Affected3.373502-1.034.02
c.1631G>AR544Q
(3D Viewer)
Likely PathogenicGAPUncertain 16-33438874-G-A16.20e-7-10.281Likely Pathogenic0.596Likely PathogenicLikely Benign0.542Likely Pathogenic0.19Likely Benign0.20.87Ambiguous0.53Ambiguous1.40Destabilizing-2.41Neutral1.000Probably Damaging0.997Probably Damaging-1.40Pathogenic0.09Tolerated3.3735111.0-28.06
c.1465C>TL489F
(3D Viewer)
Likely PathogenicGAPUncertain 26-33438497-C-T16.20e-7-12.066Likely Pathogenic0.965Likely PathogenicLikely Pathogenic0.724Likely Pathogenic1.72Ambiguous0.51.14Ambiguous1.43Ambiguous0.56Ambiguous-3.76Deleterious1.000Probably Damaging0.997Probably Damaging-1.51Pathogenic0.01Affected3.373520-1.034.02246.4-17.80.00.00.60.1XPotentially BenignThe 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.1717C>TR573W
(3D Viewer)
Likely PathogenicGAPConflicting 8-14.078Likely Pathogenic0.995Likely PathogenicLikely Pathogenic0.758Likely Pathogenic2.37Destabilizing0.70.57Ambiguous1.47Ambiguous0.88Ambiguous-6.94Deleterious1.000Probably Damaging0.997Probably Damaging-1.48Pathogenic0.00Affected3.37352-33.630.03257.639.00.10.00.20.0XXPotentially PathogenicThe 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.1741C>TR581W
(3D Viewer)
Likely PathogenicGAPUncertain 2-12.855Likely Pathogenic0.920Likely PathogenicAmbiguous0.678Likely Pathogenic1.32Ambiguous0.1-0.32Likely Benign0.50Ambiguous0.68Ambiguous-6.79Deleterious1.000Probably Damaging0.997Probably Damaging-1.37Pathogenic0.01Affected3.37342-33.630.03257.836.00.10.10.10.3XXPotentially PathogenicArg581 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.2369C>AT790NSH3-binding motifConflicting 36-33442921-C-A694.28e-5-5.243Likely Benign0.276Likely BenignLikely Benign0.103Likely Benign-2.54Deleterious0.999Probably Damaging0.997Probably Damaging2.27Pathogenic0.02Affected3.64600-2.813.00
c.1862G>AR621Q
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33440914-G-A191.18e-5-14.682Likely Pathogenic0.910Likely PathogenicAmbiguous0.621Likely Pathogenic0.81Ambiguous0.11.13Ambiguous0.97Ambiguous1.35Destabilizing-3.98Deleterious1.000Probably Damaging0.997Probably Damaging2.82Benign0.01Affected3.3735111.0-28.06243.754.30.00.0-0.40.2XXPotentially PathogenicThe 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.2443C>AR815SSH3-binding motifBenign 1-7.324In-Between0.950Likely PathogenicAmbiguous0.138Likely Benign-1.86Neutral0.999Probably Damaging0.997Probably Damaging2.67Benign0.02Affected0-13.7-69.11
c.2443C>GR815GSH3-binding motifUncertain 1-7.983In-Between0.854Likely PathogenicAmbiguous0.146Likely Benign-3.22Deleterious0.999Probably Damaging0.997Probably Damaging2.62Benign0.02Affected4.324-3-24.1-99.14
c.2444G>TR815LLikely PathogenicSH3-binding motifUncertain 1-8.546Likely Pathogenic0.865Likely PathogenicAmbiguous0.175Likely Benign-3.06Deleterious0.999Probably Damaging0.997Probably Damaging2.63Benign0.03Affected4.324-2-38.3-43.03
c.3022G>AD1008NLikely BenignLikely Benign 16-33443574-G-A31.86e-6-4.045Likely Benign0.714Likely PathogenicLikely Benign0.128Likely Benign-2.15Neutral0.999Probably Damaging0.997Probably Damaging2.75Benign0.01Affected3.775210.0-0.98
c.3023A>GD1008GUncertain 16-33443575-A-G16.20e-7-3.213Likely Benign0.742Likely PathogenicLikely Benign0.203Likely Benign-2.84Deleterious0.999Probably Damaging0.997Probably Damaging2.65Benign0.01Affected3.775-113.1-58.04
c.4003G>AG1335SLikely PathogenicConflicting 26-33451877-G-A32.37e-6-4.495Likely Benign0.986Likely PathogenicLikely Pathogenic0.362Likely Benign-3.79Deleterious1.000Probably Damaging0.997Probably Damaging2.04Pathogenic0.00Affected3.77510-0.430.03
c.862G>AD288N
(3D Viewer)
Likely PathogenicC2Uncertain 16-33437767-G-A21.24e-6-10.535Likely Pathogenic0.521AmbiguousLikely Benign0.321Likely Benign-0.39Likely Benign0.10.01Likely Benign-0.19Likely Benign-0.03Likely Benign-3.73Deleterious0.999Probably Damaging0.997Probably Damaging1.78Pathogenic0.05Affected3.3823120.0-0.98
c.910G>AD304N
(3D Viewer)
C2Uncertain 1-6.194Likely Benign0.391AmbiguousLikely Benign0.345Likely Benign0.30Likely Benign0.1-0.08Likely Benign0.11Likely Benign0.21Likely Benign-4.18Deleterious0.999Probably Damaging0.997Probably Damaging1.81Pathogenic0.03Affected3.3823120.0-0.98
c.1003C>TR335C
(3D Viewer)
Likely PathogenicC2Uncertain 16-33437908-C-T16.20e-7-14.354Likely Pathogenic0.938Likely PathogenicAmbiguous0.277Likely Benign0.53Ambiguous0.10.85Ambiguous0.69Ambiguous0.46Likely Benign-5.69Deleterious1.000Probably Damaging0.998Probably Damaging1.67Pathogenic0.01Affected3.3822-3-47.0-53.05
c.1004G>AR335H
(3D Viewer)
Likely PathogenicC2Uncertain 16-33437909-G-A21.24e-6-12.521Likely Pathogenic0.831Likely PathogenicAmbiguous0.132Likely Benign0.58Ambiguous0.10.22Likely Benign0.40Likely Benign0.72Ambiguous-3.02Deleterious1.000Probably Damaging0.998Probably Damaging1.70Pathogenic0.03Affected3.3822201.3-19.05242.482.1-2.40.6-0.10.1UncertainThe 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.1025A>CY342S
(3D Viewer)
Likely PathogenicC2Uncertain 2-7.996In-Between0.925Likely PathogenicAmbiguous0.407Likely Benign3.03Destabilizing0.12.87Destabilizing2.95Destabilizing0.93Ambiguous-6.60Deleterious1.000Probably Damaging0.998Probably Damaging1.75Pathogenic0.04Affected3.3725-3-20.5-76.10200.177.80.00.0-0.20.1Potentially PathogenicThe 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.1454G>AR485H
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33438486-G-A138.05e-6-13.628Likely Pathogenic0.948Likely PathogenicAmbiguous0.618Likely Pathogenic0.77Ambiguous0.10.12Likely Benign0.45Likely Benign1.13Destabilizing-4.97Deleterious1.000Probably Damaging0.998Probably Damaging1.93Pathogenic0.00Affected3.3735021.3-19.05
c.1468G>CA490P
(3D Viewer)
Likely PathogenicGAPUncertain 1-12.905Likely Pathogenic0.941Likely PathogenicAmbiguous0.878Likely Pathogenic-1.27Ambiguous0.11.31Ambiguous0.02Likely Benign1.07Destabilizing-4.81Deleterious1.000Probably Damaging0.998Probably Damaging-1.42Pathogenic0.01Affected3.3735-11-3.426.04
c.1474A>GK492E
(3D Viewer)
Likely PathogenicGAPConflicting 2-16.175Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.510Likely Pathogenic1.53Ambiguous0.11.90Ambiguous1.72Ambiguous1.42Destabilizing-3.98Deleterious1.000Probably Damaging0.998Probably Damaging2.99Benign0.01Affected3.3735100.40.94
c.1292T>CL431P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-14.222Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.659Likely Pathogenic6.78Destabilizing0.311.59Destabilizing9.19Destabilizing2.29Destabilizing-6.39Deleterious1.000Probably Damaging0.998Probably Damaging2.91Benign0.05Affected3.3729-3-3-5.4-16.04222.462.80.10.00.10.0XPotentially PathogenicThe 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.1304T>GL435W
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.889Likely Pathogenic0.992Likely PathogenicLikely Pathogenic0.572Likely Pathogenic2.11Destabilizing0.10.69Ambiguous1.40Ambiguous1.66Destabilizing-5.63Deleterious1.000Probably Damaging0.998Probably Damaging3.15Benign0.00Affected3.3729-2-2-4.773.05242.2-25.20.00.00.30.1XPotentially PathogenicThe 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.1855A>TT619S
(3D Viewer)
Likely PathogenicGAPUncertain 1-8.608Likely Pathogenic0.677Likely PathogenicLikely Benign0.602Likely Pathogenic1.09Ambiguous0.21.35Ambiguous1.22Ambiguous0.85Ambiguous-3.42Deleterious0.999Probably Damaging0.998Probably Damaging-1.30Pathogenic0.05Affected3.373511-0.1-14.03
c.1544G>AR515H
(3D Viewer)
Likely PathogenicGAPUncertain 16-33438787-G-A31.86e-6-10.774Likely Pathogenic0.337Likely BenignLikely Benign0.730Likely Pathogenic1.07Ambiguous0.20.74Ambiguous0.91Ambiguous1.09Destabilizing-3.44Deleterious1.000Probably Damaging0.998Probably Damaging-1.32Pathogenic0.01Affected3.3735201.3-19.05239.277.80.00.00.40.2XPotentially BenignThe 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.1556A>CE519A
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-8.557Likely Pathogenic0.904Likely PathogenicAmbiguous0.384Likely Benign-0.05Likely Benign0.00.55Ambiguous0.25Likely Benign0.00Likely Benign-5.23Deleterious0.999Probably Damaging0.998Probably Damaging3.33Benign0.10Tolerated3.37350-15.3-58.04162.483.5-0.10.1-0.20.0XPotentially BenignGlu519 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.1621G>CA541P
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.733Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.594Likely Pathogenic2.47Destabilizing0.37.26Destabilizing4.87Destabilizing0.86Ambiguous-3.16Deleterious1.000Probably Damaging0.998Probably Damaging-1.34Pathogenic0.07Tolerated3.37351-1-3.426.04170.4-11.20.10.00.10.0XPotentially PathogenicAla541 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.1639T>CC547R
(3D Viewer)
Likely PathogenicGAPUncertain 1-16.967Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.900Likely Pathogenic7.76Destabilizing0.85.83Destabilizing6.80Destabilizing1.69Destabilizing-11.60Deleterious1.000Probably Damaging0.998Probably Damaging-1.33Pathogenic0.02Affected3.3735-4-3-7.053.05267.4-90.30.00.0-0.10.1XXXXPotentially PathogenicCys547 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>AC547Y
(3D Viewer)
Likely PathogenicGAPPathogenic 1-15.871Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.874Likely Pathogenic8.53Destabilizing1.86.20Destabilizing7.37Destabilizing0.62Ambiguous-10.57Deleterious1.000Probably Damaging0.998Probably Damaging-1.33Pathogenic0.06Tolerated3.37350-2-3.860.04280.1-54.80.00.00.00.0XXXPotentially PathogenicCys547 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.2075T>AL692Q
(3D Viewer)
Likely PathogenicGAPPathogenic 1-13.873Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.596Likely Pathogenic3.24Destabilizing0.13.27Destabilizing3.26Destabilizing2.76Destabilizing-5.98Deleterious1.000Probably Damaging0.998Probably Damaging3.06Benign0.00Affected3.4217-2-2-7.314.97
c.1724G>AR575H
(3D Viewer)
GAPConflicting 46-33440776-G-A2041.27e-4-11.142Likely Pathogenic0.496AmbiguousLikely Benign0.707Likely Pathogenic0.81Ambiguous0.2-0.22Likely Benign0.30Likely Benign1.31Destabilizing-2.34Neutral1.000Probably Damaging0.998Probably Damaging-1.33Pathogenic0.05Affected3.3735201.3-19.05244.780.60.00.00.30.0XPotentially PathogenicThe 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.2245C>TR749WLikely Benign 16-33441710-C-T31.86e-6-7.647In-Between0.338Likely BenignLikely Benign0.173Likely Benign-2.62Deleterious1.000Probably Damaging0.998Probably Damaging2.59Benign0.00Affected4.3222-33.630.03
c.2443C>TR815CLikely PathogenicSH3-binding motifUncertain 16-33442995-C-T53.10e-6-9.373Likely Pathogenic0.828Likely PathogenicAmbiguous0.174Likely Benign-3.89Deleterious1.000Probably Damaging0.998Probably Damaging2.59Benign0.00Affected4.324-4-37.0-53.05
c.2444G>AR815HSH3-binding motifLikely Benign 26-33442996-G-A241.49e-5-7.474In-Between0.553AmbiguousLikely Benign0.157Likely Benign-1.81Neutral1.000Probably Damaging0.998Probably Damaging2.61Benign0.02Affected4.324201.3-19.0510.1016/j.ajhg.2020.11.011
c.2521G>AV841MUncertain 16-33443073-G-A31.86e-6-7.000In-Between0.651Likely PathogenicLikely Benign0.119Likely Benign-0.74Neutral0.999Probably Damaging0.998Probably Damaging2.54Benign0.02Affected3.77512-2.332.06
c.2143C>TP715S
(3D Viewer)
GAPLikely Pathogenic 16-33441608-C-T16.20e-7-7.635In-Between0.787Likely PathogenicAmbiguous0.277Likely Benign3.54Destabilizing0.00.81Ambiguous2.18Destabilizing0.94Ambiguous-7.17Deleterious1.000Probably Damaging0.998Probably Damaging3.43Benign0.01Affected3.5091-10.8-10.04231.8-14.0-0.10.0-0.80.1XUncertainPro715, 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.3457C>TR1153WLikely PathogenicUncertain 26-33444492-C-T21.24e-6-5.812Likely Benign0.994Likely PathogenicLikely Pathogenic0.317Likely Benign-5.88Deleterious1.000Probably Damaging0.998Probably Damaging1.46Pathogenic0.00Affected3.7752-33.630.03
c.3635C>TS1212FLikely PathogenicCoiled-coilConflicting 2-14.445Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.271Likely Benign-4.52Deleterious0.999Probably Damaging0.998Probably Damaging2.03Pathogenic0.00Affected3.775-3-23.660.10
c.3653A>TE1218VLikely PathogenicCoiled-coilUncertain 2-5.647Likely Benign0.936Likely PathogenicAmbiguous0.418Likely Benign-5.68Deleterious1.000Probably Damaging0.998Probably Damaging2.21Pathogenic0.00Affected3.775-2-27.7-29.98
c.860A>CD287A
(3D Viewer)
Likely PathogenicC2Uncertain 1-14.686Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.484Likely Benign0.30Likely Benign0.1-0.04Likely Benign0.13Likely Benign0.40Likely Benign-7.35Deleterious1.000Probably Damaging0.998Probably Damaging1.58Pathogenic0.01Affected3.3823-205.3-44.01
c.878G>AR293HLikely PathogenicC2Uncertain 1-13.009Likely Pathogenic0.973Likely PathogenicLikely Pathogenic0.438Likely Benign4.45Destabilizing2.32.12Destabilizing3.29Destabilizing0.32Likely Benign-4.60Deleterious1.000Probably Damaging0.998Probably Damaging1.45Pathogenic0.04Affected201.3-19.05
c.961C>TR321C
(3D Viewer)
Likely PathogenicC2Conflicting 26-33437866-C-T95.58e-6-10.025Likely Pathogenic0.387AmbiguousLikely Benign0.495Likely Benign0.57Ambiguous0.10.56Ambiguous0.57Ambiguous0.18Likely Benign-4.59Deleterious1.000Probably Damaging0.998Probably Damaging1.89Pathogenic0.01Affected3.3823-3-47.0-53.05
c.835C>TR279W
(3D Viewer)
Likely PathogenicC2Uncertain 1-11.417Likely Pathogenic0.942Likely PathogenicAmbiguous0.485Likely Benign2.00Destabilizing0.81.47Ambiguous1.74Ambiguous0.80Ambiguous-6.29Deleterious1.000Probably Damaging0.998Probably Damaging1.88Pathogenic0.00Affected3.39182-33.630.03270.038.30.10.00.30.0UncertainThe 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.844T>CC282R
(3D Viewer)
Likely PathogenicC2Pathogenic 2-16.378Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.466Likely Benign3.13Destabilizing0.61.58Ambiguous2.36Destabilizing1.70Destabilizing-11.03Deleterious0.999Probably Damaging0.998Probably Damaging1.63Pathogenic0.00Affected3.3918-4-3-7.053.05297.4-98.2-0.10.10.50.0XXXPotentially PathogenicThe 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.877C>TR293C
(3D Viewer)
Likely PathogenicC2Uncertain 16-33437782-C-T31.86e-6-12.844Likely Pathogenic0.985Likely PathogenicLikely Pathogenic0.579Likely Pathogenic1.38Ambiguous0.10.62Ambiguous1.00Ambiguous0.02Likely Benign-7.35Deleterious1.000Probably Damaging0.998Probably Damaging1.46Pathogenic0.00Affected3.3823-4-37.0-53.05226.096.50.00.00.10.1XXXPotentially PathogenicThe 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.895C>TR299C
(3D Viewer)
Likely PathogenicC2Conflicting 26-33437800-C-T31.86e-6-6.326Likely Benign0.572Likely PathogenicLikely Benign0.344Likely Benign1.85Ambiguous0.40.61Ambiguous1.23Ambiguous0.76Ambiguous-3.54Deleterious1.000Probably Damaging0.998Probably Damaging1.65Pathogenic0.06Tolerated3.3919-4-37.0-53.05210.791.30.10.00.00.2XXPotentially PathogenicThe 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.896G>AR299H
(3D Viewer)
C2Conflicting 26-33437801-G-A106.20e-6-7.731In-Between0.388AmbiguousLikely Benign0.238Likely Benign3.97Destabilizing1.00.94Ambiguous2.46Destabilizing1.41Destabilizing-3.35Deleterious1.000Probably Damaging0.998Probably Damaging1.69Pathogenic0.02Affected3.3919201.3-19.05211.272.5-0.10.2-0.20.3XPotentially PathogenicThe 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.962G>AR321H
(3D Viewer)
C2Uncertain 16-33437867-G-A84.96e-6-8.751Likely Pathogenic0.136Likely BenignLikely Benign0.323Likely Benign0.48Likely Benign0.1-0.36Likely Benign0.06Likely Benign0.59Ambiguous-1.43Neutral1.000Probably Damaging0.998Probably Damaging1.92Pathogenic0.25Tolerated3.3823201.3-19.05218.586.91.10.00.30.0XPotentially BenignThe 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.970C>TR324W
(3D Viewer)
Likely PathogenicC2Uncertain 16-33437875-C-T21.24e-6-12.906Likely Pathogenic0.694Likely PathogenicLikely Benign0.481Likely Benign1.49Ambiguous0.30.56Ambiguous1.03Ambiguous0.66Ambiguous-3.12Deleterious1.000Probably Damaging0.998Probably Damaging1.82Pathogenic0.16Tolerated3.39222-33.630.03256.639.10.00.10.30.2XPotentially PathogenicThe 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.1025A>GY342C
(3D Viewer)
Likely PathogenicC2Benign/Likely benign 26-33437930-A-G211.30e-5-7.596In-Between0.682Likely PathogenicLikely Benign0.404Likely Benign2.48Destabilizing0.12.73Destabilizing2.61Destabilizing0.92Ambiguous-6.67Deleterious1.000Probably Damaging0.999Probably Damaging1.72Pathogenic0.02Affected3.37250-23.8-60.04242.462.80.10.0-0.10.2Potentially PathogenicThe 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.1367A>CQ456P
(3D Viewer)
Likely PathogenicGAPUncertain 1-15.250Likely Pathogenic0.993Likely PathogenicLikely Pathogenic0.469Likely Benign3.68Destabilizing0.28.43Destabilizing6.06Destabilizing0.82Ambiguous-5.66Deleterious1.000Probably Damaging0.999Probably Damaging3.34Benign0.07Tolerated3.3734-101.9-31.01
c.1463C>TT488M
(3D Viewer)
Likely PathogenicGAPUncertain 16-33438495-C-T21.24e-6-12.459Likely Pathogenic0.973Likely PathogenicLikely Pathogenic0.746Likely Pathogenic0.66Ambiguous0.31.62Ambiguous1.14Ambiguous0.46Likely Benign-5.70Deleterious1.000Probably Damaging0.999Probably Damaging3.21Benign0.00Affected3.3735-1-12.630.09
c.1484A>GE495G
(3D Viewer)
Likely PathogenicGAPUncertain 16-33438516-A-G16.20e-7-9.400Likely Pathogenic0.923Likely PathogenicAmbiguous0.867Likely Pathogenic1.21Ambiguous0.02.06Destabilizing1.64Ambiguous0.78Ambiguous-6.70Deleterious1.000Probably Damaging0.999Probably Damaging-1.46Pathogenic0.02Affected3.3735-203.1-72.06
c.1667A>TN556I
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33438910-A-T-13.391Likely Pathogenic0.929Likely PathogenicAmbiguous0.761Likely Pathogenic0.64Ambiguous0.00.17Likely Benign0.41Likely Benign0.26Likely Benign-7.52Deleterious1.000Probably Damaging0.999Probably Damaging-1.35Pathogenic0.02Affected3.3735-3-28.0-0.94
c.1738G>AG580S
(3D Viewer)
Likely PathogenicGAPUncertain 16-33440790-G-A16.20e-7-10.788Likely Pathogenic0.861Likely PathogenicAmbiguous0.644Likely Pathogenic2.84Destabilizing0.20.59Ambiguous1.72Ambiguous0.87Ambiguous-5.73Deleterious1.000Probably Damaging0.999Probably Damaging-1.23Pathogenic0.07Tolerated3.373410-0.430.03233.9-49.30.80.00.60.1XPotentially BenignGly580 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.1487A>GE496G
(3D Viewer)
Likely PathogenicGAPUncertain 1-13.529Likely Pathogenic0.850Likely PathogenicAmbiguous0.825Likely Pathogenic1.83Ambiguous0.11.76Ambiguous1.80Ambiguous0.92Ambiguous-6.16Deleterious1.000Probably Damaging0.999Probably Damaging-1.45Pathogenic0.02Affected3.37350-23.1-72.06173.9103.10.00.0-0.70.0XXPotentially PathogenicGlu496 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.1529T>GI510S
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-11.661Likely Pathogenic0.955Likely PathogenicAmbiguous0.926Likely Pathogenic4.00Destabilizing0.13.78Destabilizing3.89Destabilizing2.34Destabilizing-4.63Deleterious1.000Probably Damaging0.999Probably Damaging-1.44Pathogenic0.00Affected3.3735-1-2-5.3-26.08201.445.9-0.40.20.00.3XPotentially PathogenicIle510 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.1579G>TD527Y
(3D Viewer)
Likely PathogenicGAPUncertain 1-15.386Likely Pathogenic0.978Likely PathogenicLikely Pathogenic0.905Likely Pathogenic-0.77Ambiguous0.21.89Ambiguous0.56Ambiguous-0.14Likely Benign-8.79Deleterious1.000Probably Damaging0.999Probably Damaging-2.41Pathogenic0.00Affected3.3735-4-32.248.09270.9-45.70.10.1-0.10.0XPotentially PathogenicAsp527 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.1787G>AR596H
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33440839-G-A159.29e-6-11.128Likely Pathogenic0.950Likely PathogenicAmbiguous0.717Likely Pathogenic3.00Destabilizing0.90.43Likely Benign1.72Ambiguous1.35Destabilizing-4.97Deleterious1.000Probably Damaging0.999Probably Damaging2.43Pathogenic0.00Affected3.3735201.3-19.05223.580.5-0.10.0-0.10.3XXPotentially PathogenicThe 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.1802C>AA601E
(3D Viewer)
Likely PathogenicGAPConflicting 2-16.752Likely Pathogenic0.992Likely PathogenicLikely Pathogenic0.588Likely Pathogenic6.68Destabilizing0.85.76Destabilizing6.22Destabilizing1.24Destabilizing-4.98Deleterious1.000Probably Damaging0.999Probably Damaging2.54Benign0.00Affected3.37350-1-5.358.04240.0-82.30.00.00.70.1XXXPotentially PathogenicThe 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.2359C>AP787TLikely PathogenicSH3-binding motifLikely Benign 16-33442911-C-A171.05e-5-4.813Likely Benign0.603Likely PathogenicLikely Benign0.258Likely Benign-4.40Deleterious1.000Probably Damaging0.999Probably Damaging2.46Pathogenic0.01Affected3.6460-10.93.99
c.2359C>TP787SSH3-binding motifUncertain 16-33442911-C-T31.86e-6-4.203Likely Benign0.564AmbiguousLikely Benign0.221Likely Benign-3.81Deleterious1.000Probably Damaging0.999Probably Damaging2.48Pathogenic0.02Affected3.646-110.8-10.04
c.2075T>CL692P
(3D Viewer)
Likely PathogenicGAPUncertain 1-16.447Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.668Likely Pathogenic9.19Destabilizing0.113.20Destabilizing11.20Destabilizing1.69Destabilizing-6.98Deleterious1.000Probably Damaging0.999Probably Damaging3.06Benign0.00Affected3.4217-3-3-5.4-16.04186.262.8-0.20.1-0.70.3XPotentially PathogenicThe 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.2729G>CG910ALikely BenignUncertain 16-33443281-G-C16.20e-7-3.587Likely Benign0.361AmbiguousLikely Benign0.209Likely Benign-1.43Neutral0.999Probably Damaging0.999Probably Damaging2.78Benign0.10Tolerated3.775102.214.03
c.3484C>TP1162SLikely BenignUncertain 1-2.118Likely Benign0.913Likely PathogenicAmbiguous0.215Likely Benign-1.93Neutral1.000Probably Damaging0.999Probably Damaging2.73Benign0.55Tolerated3.8831-10.8-10.04
c.3614T>CL1205PLikely PathogenicCoiled-coilUncertain 1-16.878Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.536Likely Pathogenic-5.91Deleterious1.000Probably Damaging0.999Probably Damaging1.45Pathogenic0.00Affected-3-3-5.4-16.04
c.3655T>CY1219HLikely PathogenicCoiled-coilUncertain 1-9.511Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.363Likely Benign-3.62Deleterious1.000Probably Damaging0.999Probably Damaging2.15Pathogenic0.00Affected3.77502-1.9-26.03
c.3721C>AL1241MCoiled-coilUncertain 1-5.881Likely Benign0.782Likely PathogenicLikely Benign0.167Likely Benign-1.43Neutral1.000Probably Damaging0.999Probably Damaging1.65Pathogenic0.00Affected42-1.918.03
c.791T>CL264P
(3D Viewer)
Likely PathogenicC2Uncertain 1-12.285Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.767Likely Pathogenic5.73Destabilizing0.36.57Destabilizing6.15Destabilizing2.65Destabilizing-6.43Deleterious1.000Probably Damaging0.999Probably Damaging0.49Pathogenic0.00Affected-3-3-5.4-16.04
c.851T>CL284PLikely PathogenicC2Likely Pathogenic1-15.588Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.794Likely Pathogenic5.83Destabilizing0.25.81Destabilizing5.82Destabilizing1.89Destabilizing-6.17Deleterious1.000Probably Damaging0.999Probably Damaging1.64Pathogenic0.00Affected-3-3-5.4-16.04
c.791T>AL264Q
(3D Viewer)
Likely PathogenicC2Uncertain 1-15.729Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.678Likely Pathogenic3.43Destabilizing0.12.41Destabilizing2.92Destabilizing2.48Destabilizing-5.52Deleterious1.000Probably Damaging0.999Probably Damaging0.49Pathogenic0.00Affected3.3818-2-2-7.314.97254.7-7.60.00.00.00.3XXXPotentially PathogenicThe 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.812C>AA271D
(3D Viewer)
Likely PathogenicC2Pathogenic 1-18.590Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.706Likely Pathogenic4.71Destabilizing0.42.67Destabilizing3.69Destabilizing1.59Destabilizing-5.52Deleterious1.000Probably Damaging0.999Probably Damaging0.62Pathogenic0.00Affected3.38190-2-5.344.01226.2-63.40.00.00.90.1XXXXPotentially PathogenicThe 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.821T>AL274Q
(3D Viewer)
Likely PathogenicC2Uncertain 1-15.518Likely Pathogenic0.995Likely PathogenicLikely Pathogenic0.774Likely Pathogenic2.54Destabilizing0.31.74Ambiguous2.14Destabilizing1.97Destabilizing-5.42Deleterious1.000Probably Damaging0.999Probably Damaging0.00Pathogenic0.00Affected3.3819-2-2-7.314.97245.91.80.00.00.10.2XXXPotentially PathogenicThe 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.859G>CD287H
(3D Viewer)
Likely PathogenicC2Likely Pathogenic 1-14.518Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.589Likely Pathogenic0.48Likely Benign0.30.32Likely Benign0.40Likely Benign0.63Ambiguous-6.43Deleterious1.000Probably Damaging0.999Probably Damaging1.51Pathogenic0.00Affected3.38231-10.322.05235.63.80.11.20.10.1XXPotentially PathogenicThe 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.859G>TD287Y
(3D Viewer)
Likely PathogenicC2Likely Pathogenic 1-12.877Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.663Likely Pathogenic0.21Likely Benign0.20.48Likely Benign0.35Likely Benign0.27Likely Benign-8.27Deleterious1.000Probably Damaging0.999Probably Damaging1.51Pathogenic0.00Affected3.3823-4-32.248.09257.8-44.4-0.61.60.20.3XXPotentially PathogenicThe 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.872A>GY291C
(3D Viewer)
Likely PathogenicC2Uncertain 1-8.997Likely Pathogenic0.967Likely PathogenicLikely Pathogenic0.505Likely Pathogenic2.90Destabilizing0.43.51Destabilizing3.21Destabilizing1.35Destabilizing-7.37Deleterious1.000Probably Damaging0.999Probably Damaging1.76Pathogenic0.01Affected3.38230-23.8-60.04205.266.10.10.0-0.40.4XXPotentially PathogenicThe 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.878G>CR293P
(3D Viewer)
Likely PathogenicC2Likely Pathogenic 1-16.275Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.497Likely Benign3.62Destabilizing0.49.06Destabilizing6.34Destabilizing0.47Likely Benign-6.43Deleterious1.000Probably Damaging0.999Probably Damaging1.45Pathogenic0.01Affected3.38230-22.9-59.07202.3132.00.10.00.10.1XXXPotentially PathogenicThe 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.917T>AV306D
(3D Viewer)
Likely PathogenicC2Uncertain 1-18.289Likely Pathogenic0.986Likely PathogenicLikely Pathogenic0.530Likely Pathogenic4.40Destabilizing0.34.29Destabilizing4.35Destabilizing2.44Destabilizing-5.44Deleterious1.000Probably Damaging0.999Probably Damaging1.74Pathogenic0.00Affected3.3819-2-3-7.715.96212.3-18.3-0.20.40.00.2XXXPotentially PathogenicThe 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.922T>CW308R
(3D Viewer)
Likely PathogenicC2Pathogenic 1-12.264Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.868Likely Pathogenic5.40Destabilizing0.54.27Destabilizing4.84Destabilizing1.88Destabilizing-12.87Deleterious1.000Probably Damaging0.999Probably Damaging0.48Pathogenic0.00Affected3.38192-3-3.6-30.03290.4-26.7-0.10.10.00.2XXXPotentially PathogenicThe 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.924G>CW308C
(3D Viewer)
Likely PathogenicC2Pathogenic/Likely path. 2-12.791Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.738Likely Pathogenic5.56Destabilizing0.34.38Destabilizing4.97Destabilizing1.26Destabilizing-11.95Deleterious1.000Probably Damaging0.999Probably Damaging0.48Pathogenic0.00Affected3.3819-8-23.4-83.07230.860.5-0.30.1-0.40.4XPotentially PathogenicThe 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.953C>TP318L
(3D Viewer)
Likely PathogenicC2Uncertain 36-33437858-C-T31.86e-6-10.090Likely Pathogenic0.958Likely PathogenicLikely Pathogenic0.624Likely Pathogenic1.33Ambiguous0.10.26Likely Benign0.80Ambiguous0.43Likely Benign-8.96Deleterious1.000Probably Damaging0.999Probably Damaging1.82Pathogenic0.03Affected3.3823-3-35.416.04228.6-68.9-0.70.7-0.40.1XPotentially BenignThe 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.980T>CL327P
(3D Viewer)
Likely PathogenicC2Pathogenic 3-16.602Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.658Likely Pathogenic5.38Destabilizing0.14.00Destabilizing4.69Destabilizing2.62Destabilizing-5.97Deleterious1.000Probably Damaging0.999Probably Damaging1.52Pathogenic0.01Affected3.3823-3-3-5.4-16.04221.769.40.10.00.60.1XPotentially PathogenicThe 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.1030G>AG344S
(3D Viewer)
Likely PathogenicC2Pathogenic 5-11.254Likely Pathogenic0.986Likely PathogenicLikely Pathogenic0.790Likely Pathogenic9.02Destabilizing0.76.08Destabilizing7.55Destabilizing0.98Ambiguous-5.28Deleterious1.000Probably Damaging1.000Probably Damaging-0.45Pathogenic0.04Affected3.372510-0.430.03217.3-51.70.00.10.20.1XXPotentially PathogenicBecause 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.1126G>TG376CC2Uncertain 1-7.686In-Between0.125Likely BenignLikely Benign0.560Likely Pathogenic2.56Destabilizing0.50.22Likely Benign1.39Ambiguous0.16Likely Benign-1.15Neutral1.000Probably Damaging1.000Probably Damaging1.32Pathogenic0.01Affected-3-32.946.09
c.1214G>CR405P
(3D Viewer)
Likely PathogenicC2Uncertain 1-14.206Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.572Likely Pathogenic3.11Destabilizing0.35.19Destabilizing4.15Destabilizing1.26Destabilizing-6.32Deleterious1.000Probably Damaging1.000Probably Damaging3.62Benign0.01Affected3.3828-202.9-59.07
c.1352T>CL451P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-14.549Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.750Likely Pathogenic6.92Destabilizing0.28.57Destabilizing7.75Destabilizing2.58Destabilizing-6.81Deleterious1.000Probably Damaging1.000Probably Damaging2.43Pathogenic0.00Affected3.3734-3-3-5.4-16.04
c.1436G>CR479P
(3D Viewer)
Likely PathogenicGAPUncertain 1-11.795Likely Pathogenic0.938Likely PathogenicAmbiguous0.277Likely Benign2.86Destabilizing0.23.88Destabilizing3.37Destabilizing0.81Ambiguous-3.52Deleterious1.000Probably Damaging1.000Probably Damaging3.41Benign0.18Tolerated0-22.9-59.07
c.1453C>AR485S
(3D Viewer)
Likely PathogenicGAPUncertain 1-15.603Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.609Likely Pathogenic0.40Likely Benign0.11.07Ambiguous0.74Ambiguous0.82Ambiguous-5.97Deleterious1.000Probably Damaging1.000Probably Damaging1.93Pathogenic0.00Affected0-13.7-69.11
c.1213C>TR405C
(3D Viewer)
Likely PathogenicC2Conflicting 26-33438118-C-T63.72e-6-9.206Likely Pathogenic0.713Likely PathogenicLikely Benign0.427Likely Benign0.72Ambiguous0.11.51Ambiguous1.12Ambiguous1.21Destabilizing-7.27Deleterious1.000Probably Damaging1.000Probably Damaging3.61Benign0.02Affected3.3828-4-37.0-53.05221.382.6-0.10.0-0.20.3XXPotentially PathogenicThe 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.1499T>CL500P
(3D Viewer)
Likely PathogenicGAPPathogenic 1-15.898Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.894Likely Pathogenic5.91Destabilizing0.38.90Destabilizing7.41Destabilizing1.92Destabilizing-6.96Deleterious1.000Probably Damaging1.000Probably Damaging-1.37Pathogenic0.01Affected3.3735-3-3-5.4-16.04
c.1513T>CY505H
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-11.383Likely Pathogenic0.982Likely PathogenicLikely Pathogenic0.646Likely Pathogenic2.91Destabilizing0.12.88Destabilizing2.90Destabilizing1.60Destabilizing-4.97Deleterious1.000Probably Damaging1.000Probably Damaging2.64Benign0.00Affected3.373520-1.9-26.03
c.1513T>GY505D
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-14.078Likely Pathogenic0.993Likely PathogenicLikely Pathogenic0.718Likely Pathogenic4.98Destabilizing0.14.72Destabilizing4.85Destabilizing2.49Destabilizing-9.95Deleterious1.000Probably Damaging1.000Probably Damaging2.60Benign0.00Affected3.3735-3-4-2.2-48.09
c.1552T>CY518H
(3D Viewer)
Likely PathogenicGAPUncertain 1-9.797Likely Pathogenic0.943Likely PathogenicAmbiguous0.496Likely Benign2.39Destabilizing0.40.82Ambiguous1.61Ambiguous1.31Destabilizing-4.74Deleterious1.000Probably Damaging1.000Probably Damaging3.40Benign0.08Tolerated02-1.9-26.03
c.1651C>AL551M
(3D Viewer)
GAPUncertain 16-33438894-C-A74.34e-6-9.937Likely Pathogenic0.480AmbiguousLikely Benign0.544Likely Pathogenic-0.07Likely Benign0.10.13Likely Benign0.03Likely Benign0.71Ambiguous-0.56Neutral1.000Probably Damaging1.000Probably Damaging-1.48Pathogenic0.06Tolerated3.373542-1.918.03246.5-18.60.00.00.30.0XPotentially BenignL551 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.1394T>CL465P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-14.824Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.778Likely Pathogenic7.18Destabilizing0.310.85Destabilizing9.02Destabilizing2.73Destabilizing-6.96Deleterious1.000Probably Damaging1.000Probably Damaging2.29Pathogenic0.00Affected3.3734-3-3-5.4-16.04211.165.90.10.0-0.20.0XPotentially PathogenicThe 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.1763T>CL588P
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.771Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.932Likely Pathogenic5.61Destabilizing0.512.91Destabilizing9.26Destabilizing2.33Destabilizing-6.97Deleterious1.000Probably Damaging1.000Probably Damaging-1.42Pathogenic0.00Affected3.3834-3-3-5.4-16.04
c.1778T>CL593P
(3D Viewer)
Likely PathogenicGAPUncertain 1-13.961Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.777Likely Pathogenic5.75Destabilizing0.910.77Destabilizing8.26Destabilizing2.43Destabilizing-6.77Deleterious1.000Probably Damaging1.000Probably Damaging2.77Benign0.00Affected-3-3-5.4-16.04
c.1453C>TR485C
(3D Viewer)
Likely PathogenicGAPUncertain 26-33438485-C-T95.58e-6-14.294Likely Pathogenic0.976Likely PathogenicLikely Pathogenic0.597Likely Pathogenic1.00Ambiguous0.10.26Likely Benign0.63Ambiguous0.44Likely Benign-7.96Deleterious1.000Probably Damaging1.000Probably Damaging1.90Pathogenic0.00Affected3.3735-4-37.0-53.05225.599.6-0.10.0-0.30.2XUncertainThe 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.1466T>CL489P
(3D Viewer)
Likely PathogenicGAPConflicting 2-13.520Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.939Likely Pathogenic2.50Destabilizing0.14.69Destabilizing3.60Destabilizing1.73Destabilizing-6.74Deleterious1.000Probably Damaging1.000Probably Damaging-1.56Pathogenic0.00Affected3.3735-3-3-5.4-16.04209.961.90.10.00.60.1XPotentially PathogenicThe 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.1784T>AL595Q
(3D Viewer)
Likely PathogenicGAPUncertain 1-15.101Likely Pathogenic0.984Likely PathogenicLikely Pathogenic0.733Likely Pathogenic0.79Ambiguous0.11.40Ambiguous1.10Ambiguous1.99Destabilizing-5.97Deleterious1.000Probably Damaging1.000Probably Damaging2.75Benign0.00Affected3.3735-2-2-7.314.97
c.1784T>CL595P
(3D Viewer)
Likely PathogenicGAPUncertain 1-11.856Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.747Likely Pathogenic2.09Destabilizing0.85.88Destabilizing3.99Destabilizing1.78Destabilizing-6.97Deleterious1.000Probably Damaging1.000Probably Damaging2.72Benign0.00Affected3.3735-3-3-5.4-16.04
c.1835A>CQ612P
(3D Viewer)
Likely PathogenicGAPUncertain 1-9.684Likely Pathogenic0.673Likely PathogenicLikely Benign0.671Likely Pathogenic-0.19Likely Benign0.33.06Destabilizing1.44Ambiguous0.56Ambiguous-5.84Deleterious1.000Probably Damaging1.000Probably Damaging-1.31Pathogenic0.19Tolerated0-11.9-31.01
c.1502T>CI501T
(3D Viewer)
Likely BenignGAPUncertain 1-5.996Likely Benign0.252Likely BenignLikely Benign0.362Likely Benign2.40Destabilizing0.11.81Ambiguous2.11Destabilizing1.57Destabilizing-3.48Deleterious1.000Probably Damaging1.000Probably Damaging3.44Benign0.16Tolerated3.37350-1-5.2-12.05214.526.90.00.00.50.0XPotentially PathogenicIle501 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.1517T>CL506P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic1-12.088Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.737Likely Pathogenic5.48Destabilizing0.710.19Destabilizing7.84Destabilizing2.50Destabilizing-6.96Deleterious1.000Probably Damaging1.000Probably Damaging1.55Pathogenic0.00Affected3.3735-3-3-5.4-16.04182.664.90.10.00.20.1XPotentially PathogenicLeu506 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.1531G>AG511R
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-11.327Likely Pathogenic0.991Likely PathogenicLikely Pathogenic0.416Likely Benign1.94Ambiguous0.31.32Ambiguous1.63Ambiguous0.94Ambiguous-7.72Deleterious1.000Probably Damaging1.000Probably Damaging3.26Benign0.06Tolerated3.3735-3-2-4.199.14279.4-159.90.00.00.70.1XXPotentially PathogenicGly511 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.1877T>CI626TLikely PathogenicGAPUncertain 1-10.420Likely Pathogenic0.946Likely PathogenicAmbiguous0.640Likely Pathogenic2.94Destabilizing0.12.70Destabilizing2.82Destabilizing2.23Destabilizing-4.18Deleterious1.000Probably Damaging1.000Probably Damaging3.04Benign0.00Affected0-1-5.2-12.05
c.1531G>CG511R
(3D Viewer)
Likely PathogenicGAPPathogenic 1-11.327Likely Pathogenic0.991Likely PathogenicLikely Pathogenic0.415Likely Benign1.94Ambiguous0.31.32Ambiguous1.63Ambiguous0.94Ambiguous-7.72Deleterious1.000Probably Damaging1.000Probably Damaging3.26Benign0.06Tolerated3.3735-3-2-4.199.14279.4-159.90.00.00.70.1XXPotentially PathogenicGly511 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.1631G>CR544P
(3D Viewer)
Likely PathogenicGAPUncertain 2-16.905Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.762Likely Pathogenic4.70Destabilizing0.14.19Destabilizing4.45Destabilizing1.14Destabilizing-4.88Deleterious1.000Probably Damaging1.000Probably Damaging-1.48Pathogenic0.05Affected3.37350-22.9-59.07192.0123.80.10.0-0.30.0XXPotentially PathogenicArg544 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.1652T>CL551P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-14.620Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.953Likely Pathogenic6.66Destabilizing0.16.58Destabilizing6.62Destabilizing2.66Destabilizing-4.70Deleterious1.000Probably Damaging1.000Probably Damaging-1.60Pathogenic0.01Affected3.3735-3-3-5.4-16.04208.660.90.10.0-0.30.0XPotentially PathogenicL551 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.1658A>CK553T
(3D Viewer)
Likely PathogenicGAPUncertain 1-15.328Likely Pathogenic0.990Likely PathogenicLikely Pathogenic0.761Likely Pathogenic1.06Ambiguous0.20.48Likely Benign0.77Ambiguous0.79Ambiguous-5.77Deleterious1.000Probably Damaging1.000Probably Damaging-1.34Pathogenic0.14Tolerated3.37350-13.2-27.07218.2-10.70.00.0-0.20.5XPotentially PathogenicLys533 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.1685C>TP562L
(3D Viewer)
Likely PathogenicGAPPathogenic/Likely path. 106-33440737-C-T-13.438Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.829Likely Pathogenic3.54Destabilizing0.80.17Likely Benign1.86Ambiguous-0.14Likely Benign-9.95Deleterious1.000Probably Damaging1.000Probably Damaging0.58Pathogenic0.00Affected3.3735-3-35.416.04228.8-68.5-0.10.00.10.2XPotentially PathogenicPro562 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.1706T>CF569S
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 2-13.384Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.916Likely Pathogenic5.70Destabilizing0.15.38Destabilizing5.54Destabilizing2.45Destabilizing-7.97Deleterious1.000Probably Damaging1.000Probably Damaging-1.32Pathogenic0.00Affected3.3734-3-2-3.6-60.10213.767.9-0.10.0-1.00.1XPotentially PathogenicPhe569 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.1714T>GW572G
(3D Viewer)
Likely PathogenicGAPUncertain 1-17.692Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.900Likely Pathogenic6.57Destabilizing0.27.57Destabilizing7.07Destabilizing1.83Destabilizing-11.98Deleterious1.000Probably Damaging1.000Probably Damaging-1.24Pathogenic0.00Affected3.3735-7-20.5-129.16195.2127.90.00.0-1.00.0XPotentially PathogenicThe 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.1715G>CW572S
(3D Viewer)
Likely PathogenicGAPPathogenic 1-17.461Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.775Likely Pathogenic5.78Destabilizing0.23.37Destabilizing4.58Destabilizing1.79Destabilizing-12.74Deleterious1.000Probably Damaging1.000Probably Damaging-1.24Pathogenic0.01Affected3.3735-2-30.1-99.14235.176.60.00.0-0.40.1XPotentially PathogenicThe 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.1718G>TR573L
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-13.120Likely Pathogenic0.993Likely PathogenicLikely Pathogenic0.833Likely Pathogenic1.30Ambiguous0.61.11Ambiguous1.21Ambiguous0.80Ambiguous-5.74Deleterious1.000Probably Damaging1.000Probably Damaging-1.41Pathogenic0.01Affected3.3735-3-28.3-43.03237.460.70.00.0-0.70.3XXPotentially PathogenicThe 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.1723C>TR575C
(3D Viewer)
Likely PathogenicGAPConflicting 36-33440775-C-T231.43e-5-11.179Likely Pathogenic0.630Likely PathogenicLikely Benign0.715Likely Pathogenic1.39Ambiguous0.20.50Ambiguous0.95Ambiguous0.73Ambiguous-5.43Deleterious1.000Probably Damaging1.000Probably Damaging-1.30Pathogenic0.02Affected3.3735-4-37.0-53.05227.799.20.00.00.00.1XPotentially PathogenicThe 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.1763T>AL588H
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-16.947Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.939Likely Pathogenic4.20Destabilizing0.23.69Destabilizing3.95Destabilizing2.26Destabilizing-6.97Deleterious1.000Probably Damaging1.000Probably Damaging-1.42Pathogenic0.00Affected3.3834-2-3-7.023.98214.320.90.00.00.00.2XXXPotentially PathogenicThe 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.1767C>GI589M
(3D Viewer)
Likely PathogenicGAPUncertain 1-12.225Likely Pathogenic0.926Likely PathogenicAmbiguous0.830Likely Pathogenic0.74Ambiguous0.21.54Ambiguous1.14Ambiguous1.33Destabilizing-2.99Deleterious1.000Probably Damaging1.000Probably Damaging-1.94Pathogenic0.00Affected3.373521-2.618.03267.6-24.50.00.0-0.10.1XPotentially BenignA 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.1778T>AL593H
(3D Viewer)
Likely PathogenicGAPUncertain 1-16.504Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.812Likely Pathogenic2.52Destabilizing0.22.32Destabilizing2.42Destabilizing2.75Destabilizing-6.77Deleterious1.000Probably Damaging1.000Probably Damaging2.77Benign0.00Affected3.3735-2-3-7.023.98222.020.70.00.00.20.0XXPotentially PathogenicThe 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.1786C>TR596C
(3D Viewer)
Likely PathogenicGAPConflicting 26-33440838-C-T63.72e-6-10.805Likely Pathogenic0.972Likely PathogenicLikely Pathogenic0.633Likely Pathogenic2.94Destabilizing0.01.49Ambiguous2.22Destabilizing-0.03Likely Benign-7.96Deleterious1.000Probably Damaging1.000Probably Damaging2.41Pathogenic0.00Affected3.3735-4-37.0-53.05230.797.9-0.10.0-0.30.4XXPotentially PathogenicThe 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.1787G>TR596L
(3D Viewer)
Likely PathogenicGAPUncertain 1-13.197Likely Pathogenic0.992Likely PathogenicLikely Pathogenic0.756Likely Pathogenic1.51Ambiguous0.3-0.58Ambiguous0.47Likely Benign-0.02Likely Benign-6.97Deleterious1.000Probably Damaging1.000Probably Damaging2.45Pathogenic0.00Affected3.3735-3-28.3-43.03234.263.4-0.10.0-0.50.6XXPotentially PathogenicThe 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.1813C>TP605S
(3D Viewer)
Likely PathogenicGAPUncertain 1-10.830Likely Pathogenic0.987Likely PathogenicLikely Pathogenic0.718Likely Pathogenic3.40Destabilizing0.13.34Destabilizing3.37Destabilizing1.00Destabilizing-7.96Deleterious1.000Probably Damaging1.000Probably Damaging0.70Pathogenic0.00Affected3.37351-10.8-10.04213.8-15.4-0.30.20.20.1XXPotentially PathogenicPro605 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.1814C>GP605R
(3D Viewer)
Likely PathogenicGAPUncertain 1-13.745Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.845Likely Pathogenic8.71Destabilizing2.56.46Destabilizing7.59Destabilizing0.92Ambiguous-8.95Deleterious1.000Probably Damaging1.000Probably Damaging0.69Pathogenic0.00Affected3.37350-2-2.959.07281.7-118.1-0.20.00.50.1XXXXPotentially PathogenicPro605 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.1898T>CL633P
(3D Viewer)
Likely PathogenicGAPPathogenic/Likely path. 2-15.669Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.693Likely Pathogenic6.60Destabilizing0.210.15Destabilizing8.38Destabilizing2.42Destabilizing-6.97Deleterious1.000Probably Damaging1.000Probably Damaging2.70Benign0.00Affected3.3734-3-3-5.4-16.04193.265.10.00.00.10.0XPotentially PathogenicThe 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.2087T>CL696P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-16.926Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.678Likely Pathogenic6.66Destabilizing0.210.84Destabilizing8.75Destabilizing2.13Destabilizing-6.58Deleterious1.000Probably Damaging1.000Probably Damaging3.00Benign0.00Affected3.4613-3-3-5.4-16.04180.665.90.10.0-0.60.1XPotentially PathogenicThe 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.2162T>GI721S
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.032Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.466Likely Benign3.91Destabilizing0.13.96Destabilizing3.94Destabilizing2.28Destabilizing-5.26Deleterious1.000Probably Damaging1.000Probably Damaging2.21Pathogenic0.00Affected3.509-1-2-5.3-26.08203.349.3-0.10.0-1.10.0XUncertainThe 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.2681G>AG894ELikely BenignUncertain 16-33443233-G-A63.72e-6-5.377Likely Benign0.859Likely PathogenicAmbiguous0.180Likely Benign-2.07Neutral1.000Probably Damaging1.000Probably Damaging2.68Benign0.01Affected4.3240-2-3.172.06

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