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.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.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.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.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.1066C>TR356C
(3D Viewer)
Likely PathogenicC2Likely Benign 16-33437971-C-T53.10e-6-11.827Likely Pathogenic0.774Likely PathogenicLikely Benign0.312Likely Benign0.76Ambiguous0.01.19Ambiguous0.98Ambiguous0.84Ambiguous-7.12Deleterious1.000Probably Damaging0.990Probably Damaging1.67Pathogenic0.00Affected3.3922-4-37.0-53.05212.391.0-0.10.3-0.30.1XPotentially PathogenicArg356 is located in a loop that includes a short helical section and connects two anti-parallel β sheet strands (res. Gly341-Pro349, res. Thr359-Pro364). In the WT simulations, the guanidinium group of Arg356 alternately forms salt bridges with the carboxylate groups of the GAP domain residues, Glu446 and Glu698. Arg356 also forms hydrogen bonds with the hydroxyl group of the GAP domain residue Thr691 and interacts with Met409 at the C2-GAP interface.In the variant simulations, the Cys356 mutation fails to maintain any of the Arg356 interactions and only occasionally forms weak hydrogen bonds with nearby C2 domain residues (e.g., Gln407). Although no negative structural effects are observed during the simulations, Arg356 is located at the C2 and GAP domain interface, making the residue swap potentially detrimental to the tertiary structure assembly.
c.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.1193C>TP398L
(3D Viewer)
C2Uncertain 16-33438098-C-T84.96e-6-7.518In-Between0.547AmbiguousLikely Benign0.599Likely Pathogenic1.48Ambiguous0.2-0.54Ambiguous0.47Likely Benign0.62Ambiguous-7.10Deleterious0.961Probably Damaging0.256Benign5.72Benign0.01Affected3.4016-3-35.416.04245.8-68.6-0.10.0-0.30.2XPotentially PathogenicPro398 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. Although the residue swap does not influence the nearby secondary structure elements, proline is often found at the ends of β sheets due to its disfavored status during folding.Additionally, the Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone. Ω loops are known to play significant roles in protein functions that require flexibility, and thus hydrophobic residues like leucine are rarely tolerated. Although no negative structural effects are visualized in the variant’s simulations, Leu398 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. Since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1195G>AA399T
(3D Viewer)
Likely BenignC2Benign 1-5.236Likely Benign0.114Likely BenignLikely Benign0.272Likely Benign1.24Ambiguous0.10.91Ambiguous1.08Ambiguous0.49Likely Benign-0.40Neutral0.131Benign0.039Benign5.41Benign0.69Tolerated3.382610-2.530.03211.4-41.40.00.00.60.4XPotentially PathogenicThe methyl group of Ala399, located in an anti-parallel β sheet strand (res. Ala399-Ile411), is swapped for a hydroxyl-containing threonine. In the variant simulations, the hydroxyl group of Thr399 can form H-bonds with the backbone atoms of the residues in the membrane-facing loops (e.g., Gly382) in the C2 domain. Consequently, the ability of the Thr399 side chain to form H-bonds with the membrane-facing loops could adversely affect the dynamics and stability of the SynGAP-membrane association. However, since the effects on the dynamics of the membrane-facing loops can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1199T>AV400E
(3D Viewer)
Likely PathogenicC2Uncertain 1-13.686Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.810Likely Pathogenic3.70Destabilizing0.22.46Destabilizing3.08Destabilizing2.29Destabilizing-4.88Deleterious0.920Possibly Damaging0.335Benign5.31Benign0.00Affected3.3827-2-2-7.729.98249.1-38.8-0.10.11.00.0XXXPotentially PathogenicThe iso-propyl side chain of Val400, located in an anti-parallel β sheet strand (res. Ala399-Ile411), hydrophobically packs against hydrophobic residues within the anti-parallel β sheet of the C2 domain (e.g., Ile268, Ala404, Leu325, Leu402). In the variant simulations, the negatively charged carboxylate group of the Glu400 side chain is not suitable for occupying the hydrophobic niche. Consequently, the side chain escapes the center of the C2 domain and interacts with the backbone amide groups of Leu402 in the same β strand and/or Ile269 and Glu270 in a neighboring β strand (res. Arg259-Arg272). This residue swap disrupts the hydrophobic packing and generally has extensive negative effects on the C2 domain structure. At a minimum, the residue swap could affect the C2 domain stability and membrane association.
c.1205T>GL402R
(3D Viewer)
Likely PathogenicC2Likely Pathogenic1-13.800Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.522Likely Pathogenic4.10Destabilizing0.23.82Destabilizing3.96Destabilizing2.24Destabilizing-4.69Deleterious0.967Probably Damaging0.459Possibly Damaging3.69Benign0.00Affected3.3828-3-2-8.343.03259.5-55.40.00.01.40.0XXXPotentially PathogenicThe iso-butyl side chain of Leu402, located in an anti-parallel β sheet strand (res. Ala399-Ile411), packs with residues inside the hydrophobic core of the C2 domain (e.g., Ile268, Ala404, Leu266, Val400). In the variant simulations, the positively charged guanidinium group of the Arg402 side chain is not suitable for the hydrophobic niche. Consequently, the side chain moves outward from the hydrophobic C2 domain core and stacks with the phenol ring of Tyr363 or forms H-bonds with the carboxamide group of the Gln361 side chain in the β sheet strand (res. Thr359-Tyr364). This movement induces extensive negative effects on the C2 domain structure.
c.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.1214G>AR405H
(3D Viewer)
Likely PathogenicC2Conflicting 26-33438119-G-A42.48e-6-9.081Likely Pathogenic0.706Likely PathogenicLikely Benign0.371Likely Benign2.79Destabilizing0.61.85Ambiguous2.32Destabilizing1.26Destabilizing-4.54Deleterious1.000Probably Damaging0.991Probably Damaging3.65Benign0.01Affected3.3828201.3-19.05214.0102.2-0.10.0-0.70.1XPotentially PathogenicThe guanidinium group of Arg405, located in an anti-parallel β sheet strand of the C2 domain (res. Pro398-Ile411), forms a salt bridge with the carboxylate group of the Glu446 side chain from an opposing α helix (res. Val441-Ser457) in the GAP domain. The positively charged Arg405 side chain also stacks with the aromatic ring of the Phe358 side chain from a loop preceding the β strand (res. Thr359-Thr366), which could assist in maintaining the anti-parallel strand arrangement.In the variant simulations, the imidazole ring of His405 does not stack with the aromatic ring of Phe358 nor form any lasting H-bonds with the loop residues. The imidazole ring of His405 (neutral and epsilon protonated in the simulations) is unable to form a salt bridge with Glu446, which could affect the tertiary structure assembly, although this is not apparent based on the variant simulations.
c.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.1259T>CF420S
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-13.231Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.544Likely Pathogenic5.34Destabilizing0.15.73Destabilizing5.54Destabilizing2.14Destabilizing-7.43Deleterious0.998Probably Damaging0.938Probably Damaging3.09Benign0.00Affected3.3729-3-2-3.6-60.10213.357.80.00.0-0.40.1XPotentially PathogenicIn the WT, the phenyl ring of the Phe420 side chain, located on an α helix (res. Met414-Glu436), packs against hydrophobic residues in the interhelix area of the GAP domain (e.g., Leu689, Leu714, Leu717, Leu718). Although no large-scale adverse effects are seen in the variant simulations, the polar hydroxyl group of Ser420 is not suitable for the hydrophobic inter-helix space. Thus, the residue swap could affect protein folding. In theory, the introduced hydroxyl group could also lower the α helix integrity by H-bonding with the backbone atoms of neighboring residues in the same α helix. However, no such effect is seen in the variant simulations.
c.1285C>TR429W
(3D Viewer)
GAPConflicting 56-33438190-C-T654.03e-5-10.666Likely Pathogenic0.500AmbiguousLikely Benign0.282Likely Benign0.31Likely Benign0.1-0.13Likely Benign0.09Likely Benign0.52Ambiguous-3.19Deleterious1.000Probably Damaging0.990Probably Damaging3.41Benign0.03Affected3.38252-33.630.03252.345.50.00.00.20.1XPotentially PathogenicThe guanidinium group of Arg429, located in an α helix (res. Met414-Glu436), either forms a salt bridge with the carboxylate group of an acidic residue (Asp474, Asp467) or a H-bond with the hydroxyl group of Ser471 in an opposing α helix (res. Ala461-Phe476). In the variant simulations, the indole ring of the Trp429 side chain cannot form ionic interactions with the acidic residues. Although it forms a H-bond with Ser471, the bonding is not as strong as that of arginine. The residue swap could affect the tertiary structure assembly during folding; however, no large-scale negative effects were seen during the simulations.
c.1286G>AR429Q
(3D Viewer)
Likely BenignGAPUncertain 26-33438191-G-A106.20e-6-8.227Likely Pathogenic0.143Likely BenignLikely Benign0.156Likely Benign0.45Likely Benign0.10.36Likely Benign0.41Likely Benign0.98Ambiguous-1.25Neutral1.000Probably Damaging0.979Probably Damaging3.47Benign0.58Tolerated3.3825111.0-28.06235.859.50.00.0-0.30.4XPotentially PathogenicThe guanidinium group of the Arg429 side chain, located in an α helix (res. Met414-Glu436), either forms a salt bridge with the carboxylate group of an acidic residue (Asp474, Asp467) or an H-bond with the hydroxyl group of Ser471 in an opposing α helix (res. Ala461-Phe476). In the variant simulations, Gln429 cannot form ionic interactions with the acidic residues; however, the carboxamide group can form multiple H-bonds. The H-bonding coordination of the Asn429 side chain varied between the replica simulations. In one simulation, three H-bonds were formed simultaneously with the Asp467 side chain, the backbone carbonyl group of Asn426, and the amide group of Met430 at the end of the same α helix. The residue swap could affect the tertiary structure assembly during folding due to weaker bond formation, but no large-scale negative effects were seen during the simulations.
c.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.1306G>AE436K
(3D Viewer)
Likely PathogenicGAPUncertain 1-13.869Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.829Likely Pathogenic0.56Ambiguous0.12.86Destabilizing1.71Ambiguous0.82Ambiguous-3.77Deleterious0.994Probably Damaging0.951Probably Damaging4.71Benign0.02Affected3.372901-0.4-0.94186.839.80.00.0-0.20.0XXXPotentially PathogenicThe carboxylate group of Glu436, located on the α helix (res. Met414-Glu436), forms a salt bridge with the amino group of the Lys444 side chain on an opposing α helix (res. Val441-Ser457). The backbone carbonyl of Glu436 also H-bonds with the Lys444 side chain, which helps keep the ends of the two α helices tightly connected. In contrast, in the variant simulations, the salt bridge formation with Lys444 is not possible. Instead, the repelled Lys436 side chain rotates outward, causing a change in the α helix backbone H-bonding: the amide group of Lys444 H-bonds with the carbonyl of Ala433 instead of the carbonyl of Cys432.
c.1622C>GA541G
(3D Viewer)
GAPUncertain 16-33438865-C-G21.24e-6-7.233In-Between0.341AmbiguousLikely Benign0.421Likely Benign0.67Ambiguous0.00.94Ambiguous0.81Ambiguous0.76Ambiguous-1.48Neutral0.999Probably Damaging0.995Probably Damaging-1.31Pathogenic0.57Tolerated3.373510-2.2-14.03170.123.60.00.00.00.0XPotentially 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. Glycine, known as an “α-helix breaker,” weakens the integrity of the helix. Indeed, in the variant simulations, the hydrogen bond formation between Gly541 and the backbone carbonyl of Ala537 is disrupted.
c.1349C>AA450E
(3D Viewer)
Likely PathogenicGAPUncertain 1-16.578Likely Pathogenic0.989Likely PathogenicLikely Pathogenic0.653Likely Pathogenic3.86Destabilizing0.25.23Destabilizing4.55Destabilizing1.59Destabilizing-4.67Deleterious0.999Probably Damaging0.992Probably Damaging3.38Benign0.07Tolerated3.37320-1-5.358.04240.1-82.60.00.00.70.0XXPotentially PathogenicThe methyl group of Ala450, located in an α helix (res. Asn440-Thr458), packs against hydrophobic residues in the inter-helix space (e.g., Leu692). In the variant simulations, the carboxylate group of the Glu450 side chain rotates outward, away from the hydrophobic niche, where it does not form any lasting salt bridges or H-bonds. Although the residue swap does not negatively affect the protein structure based on the simulations, it is possible that the introduction of the negatively charged residue adversely affects the folding process or tertiary assembly.
c.1354G>TV452F
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.769Likely Pathogenic0.975Likely PathogenicLikely Pathogenic0.511Likely Pathogenic9.21Destabilizing0.10.37Likely Benign4.79Destabilizing0.61Ambiguous-4.94Deleterious0.999Probably Damaging0.993Probably Damaging3.29Benign0.00Affected3.3734-1-1-1.448.04249.4-35.70.00.00.40.1XPotentially PathogenicThe iso-propyl side chain of Val452, located in the middle of an α helix (res. Val441-Ser457), packs against hydrophobic residues in the inter-helix space at the intersection of three α helices (e.g., Leu500, His453, Leu465). In the variant simulations, the larger side chain of Phe452 cannot pack against the opposing α helix (res. Leu489-Glu519) as efficiently as valine. Due to space restrictions, the phenol ring adjusts to make room by rotating slightly sideways in the inter-helix space. Besides this small and local shift, no large-scale effects on the protein structure are seen based on the simulations. However, the size difference between the swapped residues could affect the protein folding process.
c.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.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.1403T>AM468K
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-16.982Likely Pathogenic0.978Likely PathogenicLikely Pathogenic0.828Likely Pathogenic3.21Destabilizing0.13.30Destabilizing3.26Destabilizing2.57Destabilizing-4.61Deleterious0.878Possibly Damaging0.922Probably Damaging-1.34Pathogenic0.04Affected3.37310-1-5.8-3.02188.769.30.00.0-0.10.2XXPotentially PathogenicThe thioether group of Met468, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues (e.g., Phe464, Leu465, Leu489) in an inter-helix space formed by two other α helices (res. Ala461–Phe476, res. Thr488–Gly502). In the variant simulations, the positively charged side chain of Lys468 rotates outward to escape the hydrophobic niche, forming an H-bond with the hydroxyl group of the Ser471 side chain and a salt bridge with the carboxylate group of the Glu472 side chain. This residue swap also disrupts the methionine-aromatic stacking with the phenyl ring of the Phe464 side chain. Although no large-scale structural changes are observed during the variant simulations, the importance of hydrophobic packing suggests that the effects could be more pronounced during protein folding.
c.1403T>CM468T
(3D Viewer)
Likely PathogenicGAPUncertain 26-33438435-T-C16.20e-7-12.399Likely Pathogenic0.862Likely PathogenicAmbiguous0.801Likely Pathogenic3.47Destabilizing0.13.10Destabilizing3.29Destabilizing1.84Destabilizing-3.85Deleterious0.994Probably Damaging0.985Probably Damaging-1.31Pathogenic0.01Affected3.3731-1-1-2.6-30.09214.647.10.00.00.10.0XPotentially PathogenicThe thioether group of Met468, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues (e.g., Phe464, Leu465, Leu489) in an inter-helix space formed by two other α helices (res. Ala461–Phe476, res. Thr488–Gly502). In the variant simulations, the hydrophilic side chain of Thr468 does not pack favorably in the hydrophobic niche, and the methionine-aromatic stacking is lost. Although the hydroxyl group of Thr468 forms an H-bond with the backbone carbonyl group of Phe464, the integrity of the α helix is not affected in the simulations. No large-scale structural changes are observed during the variant simulations; however, due to the importance of hydrophobic packing, the effects could be more pronounced during protein folding.
c.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.1409T>CM470T
(3D Viewer)
Likely PathogenicGAPUncertain 1-8.104Likely Pathogenic0.976Likely PathogenicLikely Pathogenic0.763Likely Pathogenic3.19Destabilizing0.12.68Destabilizing2.94Destabilizing1.49Destabilizing-5.30Deleterious0.996Probably Damaging0.985Probably Damaging-1.08Pathogenic0.24Tolerated3.3734-1-1-2.6-30.09213.846.50.00.0-0.20.2XXPotentially PathogenicThe thioether group of Met470, located in the middle of an α helix (res. Ala461–Phe476), interacts with hydrophobic residues in the inter-helix space (e.g., Val473, Leu558, Cys576, Trp572) formed by two other α helices (res. Ser604–Arg581, res. Pro562–Arg579). In the WT simulations, the Met470 side chain also packs against the positively charged guanidinium groups of Arg575, Arg429, and Arg579, which form salt bridges with the negatively charged carboxylate groups of the Asp474 and Asp467 side chains at the protein surface. In the variant simulations, the hydroxyl group of the Thr470 side chain forms an H-bond with the backbone carbonyl group of Ser466 in the α helix, potentially lowering its structural integrity. Importantly, the hydroxyl group of Thr470 also forms an H-bond with the guanidinium group of Arg575, which helps it form a more permanent salt bridge with Asp467.
c.1423C>TR475W
(3D Viewer)
Likely PathogenicGAPUncertain 16-33438455-C-T16.20e-7-13.235Likely Pathogenic0.962Likely PathogenicLikely Pathogenic0.725Likely Pathogenic1.44Ambiguous0.4-0.92Ambiguous0.26Likely Benign0.56Ambiguous-7.56Deleterious1.000Probably Damaging0.995Probably Damaging-1.45Pathogenic0.00Affected3.39282-33.630.03266.939.60.00.00.00.1XXXPotentially PathogenicIn the WT simulations, the guanidinium group of Arg475, located near the end of an α-helix (res. Ala461-Phe476), stacks with the phenyl ring of Phe476 and forms a salt bridge with Glu472. Additionally, Arg475 occasionally forms another salt bridge with the carboxylate group of Glu486 on the α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. Therefore, Arg475 potentially plays a key role in positioning the loop by interacting with Glu486, which is necessary for the positioning of the “arginine finger” (Arg485) and, ultimately, for RasGTPase activation.In the variant simulations, Trp475 moves and stacks with Arg479 on the proceeding α-α loop, disrupting the terminal end of the α-helix. Lastly, the potential effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1424G>AR475Q
(3D Viewer)
Likely PathogenicGAPUncertain 26-33438456-G-A53.10e-6-12.087Likely Pathogenic0.721Likely PathogenicLikely Benign0.632Likely Pathogenic0.71Ambiguous0.10.12Likely Benign0.42Likely Benign0.82Ambiguous-3.65Deleterious1.000Probably Damaging0.991Probably Damaging-1.32Pathogenic0.01Affected3.3928111.0-28.06253.652.70.00.0-0.80.0XXXPotentially PathogenicIn the WT simulations, the guanidinium group of Arg475, located near the end of an α-helix (res. Ala461-Phe476), stacks with the phenyl ring of Phe476 and forms a salt bridge with Glu472. Additionally, Arg475 occasionally forms another salt bridge with the carboxylate group of Glu486 on the α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. Therefore, Arg475 potentially plays a key role in positioning the loop by interacting with Glu486, which is necessary for the positioning of the “arginine finger” (Arg485) and, ultimately, for RasGTPase activation. In the variant simulations, Asn475 forms a hydrogen bond with Arg479 on the proceeding α-α loop. The absence of Phe476/Arg475 stacking and the Arg475-Glu472 salt bridge weakens the integrity of the terminal end of the α-helix during the variant simulations. Lastly, the potential effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.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.1481T>GI494R
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-15.758Likely Pathogenic0.995Likely PathogenicLikely Pathogenic0.911Likely Pathogenic6.71Destabilizing0.33.40Destabilizing5.06Destabilizing2.19Destabilizing-6.43Deleterious0.999Probably Damaging0.957Probably Damaging-1.41Pathogenic0.00Affected3.3735-2-3-9.043.03273.9-59.80.00.00.00.1XXXXPotentially PathogenicThe sec-butyl side chain of Ile494, located in an α-helix (res. Leu489-Glu519), packs against hydrophobic residues (e.g., Phe484, Leu465, Trp572, Ala493, Met468) in an inter-helix space (res. Leu489-Glu519 and res. Ala461-Phe476). In the variant simulations, the bulkier and positively charged residue, Arg494, weakens the integrity of the opposing helix. Additionally, the bulkier Arg494 stacks with Phe484, causing the α-helices to move farther apart to accommodate it. This mutation could have substantial negative effects due to the fundamental role of hydrophobic packing, which is disrupted by Arg494 during protein folding.
c.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.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.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.1505G>AG502D
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.796Likely Pathogenic0.994Likely PathogenicLikely Pathogenic0.915Likely Pathogenic3.79Destabilizing0.95.69Destabilizing4.74Destabilizing1.38Destabilizing-6.80Deleterious0.999Probably Damaging0.977Probably Damaging-1.66Pathogenic0.00Affected3.37351-1-3.158.04224.2-80.0-0.80.70.60.3XXXPotentially PathogenicGly502 is located in a hinge in the middle of an α-helix (res. Leu489-Glu519). In the WT, Gly502 acts as an α-helix breaker due to its lack of a side chain, facilitating a bend in the middle of the α-helix. In the variant simulations, the carboxylate group of Asp502 forms hydrogen bonds with neighboring residues (e.g., Ser677, Lys504), disrupting the hinge. Additionally, Asp502 struggles to fit into the α-helix hinge and cannot generate a similar bend as Gly502, which would drastically affect the secondary structure during folding. Thus, the deleterious effect seen in the simulations is likely an underestimate of the impact of the residue swap on the protein structure during protein folding.
c.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.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.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.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.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.1973G>AG658D
(3D Viewer)
GAPUncertain 16-33441232-G-A31.86e-6-7.786In-Between0.442AmbiguousLikely Benign0.144Likely Benign-0.40Likely Benign0.1-0.59Ambiguous-0.50Ambiguous0.46Likely Benign-2.64Deleterious0.008Benign0.005Benign3.53Benign0.38Tolerated3.39241-1-3.158.04219.8-84.30.00.00.20.1XPotentially PathogenicGly658, located on the outer surface of an α helix (res. Ser641-Glu666), weakens the helix integrity at that spot, which is necessary for the kink in the middle of the long helix. In the variant simulations, the carboxylic acid side chain of Asp658 is on the surface of the α helix and is not involved in any interactions. However, aspartate is not as effective a breaker of the secondary structure element as glycine, which may lead to misfolding.
c.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.1625A>GN542S
(3D Viewer)
Likely PathogenicGAPLikely Benign 1-9.675Likely Pathogenic0.767Likely PathogenicLikely Benign0.752Likely Pathogenic0.98Ambiguous0.10.99Ambiguous0.99Ambiguous0.91Ambiguous-4.40Deleterious1.000Probably Damaging0.989Probably Damaging-1.36Pathogenic0.13Tolerated3.3735112.7-27.03212.532.10.00.0-0.60.3XPotentially PathogenicAsn542 is located in an α-helix (res. Ala533-Val560) next to an α-α loop between two α-helices (res. Gly502-Tyr518 and Ala533-Val560). In the WT simulations, the carboxamide group of the Asn542 side chain forms a hydrogen bond with the backbone carbonyl group of Asn523 and packs favourably against Glu522 from the loop. In contrast, in the variant simulations, the hydroxyl group of the Ser542 side chain is unable to maintain either the hydrogen bond with Asn523 or the packing against the Glu522 side chain. Instead, the hydroxyl group of Ser542 occasionally forms a hydrogen bond with the backbone carbonyl group of Glu538.Altogether, the residue swap results in a looser helix-loop association, which is especially evident in the third replica simulation, where Asn523 moves away from its initial placement next to the α-helix. In short, based on the simulations, the residue swap weakens the GAP domain tertiary structure assembly, which in turn could negatively affect protein folding.
c.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.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.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>CW572R
(3D Viewer)
Likely PathogenicGAPNot provided1-17.511Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.894Likely Pathogenic4.84Destabilizing0.16.19Destabilizing5.52Destabilizing1.79Destabilizing-12.81Deleterious-1.25Pathogenic0.00Affected3.37352-3-3.6-30.03312.6-37.60.00.0-1.00.0XXPotentially PathogenicThe indole ring of Trp572, located in an α-helix (res. Arg563-Glu578), lies in a hydrophobic inter-helix space, where it makes extensive hydrophobic interactions with nearby residues such as Met470, Phe569, Leu588, and Ile589. The guanidinium group of Arg572 is similarly sized to the tryptophan it replaced; however, it is also positively charged. In the variant simulations, Arg572 forms hydrogen bonds with other residues in the inter-helix space, such as Ser592 and the backbone carbonyl atom of Leu465. Additionally, Arg572 hydrophobically packs its carbon chain with surrounding residues such as Phe569 and Ile589.However, the introduced residue arginine is too hydrophilic and charged for the hydrophobic space, disrupting the hydrophobic packing of the inter-helix space. Indeed, in the second simulation, Arg572 successfully escapes the hydrophobic niche completely, causing the whole protein to partially unfold.Overall, the residue swap is highly likely to cause critical protein folding problems, as evidenced by the effects seen in the variant simulations.
c.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.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.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.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.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.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.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.1760G>CR587T
(3D Viewer)
Likely PathogenicGAPUncertain 1-9.697Likely Pathogenic0.784Likely PathogenicLikely Benign0.603Likely Pathogenic1.14Ambiguous0.20.74Ambiguous0.94Ambiguous0.98Ambiguous-4.71Deleterious0.998Probably Damaging0.847Possibly Damaging-1.19Pathogenic0.08Tolerated3.3735-1-13.8-55.08227.287.40.00.00.50.1XPotentially PathogenicThe guanidinium group of Arg587, located on an α helix (res. Glu582-Met603), is constantly rotating and breaking/forming multiple hydrogen bonds and/or salt bridges at the surface intersection of α helices in the WT simulations. The positively charged Arg587 side chain can form a salt bridge with either the carboxylate group of Asp583 or Asp586 in the same helix, or with Glu480 on the opposing short helical loop structure (res. Glu480-Leu482).Importantly, the Arg587 side chain also hydrogen bonds with the backbone carbonyl groups of Ala634 and Asn635, as well as the carboxamide group of Asn635 at the end of another α helix (res. Asp616-Phe636). However, in the variant simulations, the neutral hydroxyl group of the Thr587 side chain is unable to form these salt bridges. Due to its smaller size, it also does not form the hydrogen bonds that the Arg587 side chain could. Instead, the hydroxyl group of Thr587 hydrogen bonds with the backbone carbonyl group of Asp583, which could weaken the integrity of the α helix, although this is not observed in the simulations.Overall, the residue swap could weaken the tertiary structure assembly and negatively affect the overall protein folding process.
c.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.1768A>GS590G
(3D Viewer)
Likely PathogenicGAPConflicting 26-33440820-A-G148.67e-6-14.277Likely Pathogenic0.574Likely PathogenicLikely Benign0.379Likely Benign0.67Ambiguous0.11.28Ambiguous0.98Ambiguous0.71Ambiguous-3.92Deleterious1.000Probably Damaging0.922Probably Damaging3.42Benign0.06Tolerated3.3735100.4-30.03186.749.40.00.00.10.0XPotentially PathogenicIn the WT simulations, the hydroxyl group of Ser590, located on an α helix (res. Glu582-Met603), forms hydrogen bonds with the backbone carbonyl of Ala634 and/or the carboxamide group of the Asn635 side chain at the end of the opposing α helix (res. Thr619-Ala634).The residue swap could weaken the integrity of the α helix, as glycine is known as an “α helix breaker.” However, no discernible difference was observed between the WT and variant simulations in this regard. Importantly, Gly590 cannot form hydrogen bonds with the opposing helix in the same way that serine can, which could weaken the tertiary structure assembly between the two helices.
c.1771G>CA591P
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.479Likely Pathogenic0.991Likely PathogenicLikely Pathogenic0.404Likely Benign3.78Destabilizing0.37.29Destabilizing5.54Destabilizing1.45Destabilizing-4.41Deleterious0.995Probably Damaging0.853Possibly Damaging3.35Benign0.01Affected3.37351-1-3.426.04191.5-10.10.20.10.40.1XPotentially PathogenicThe methyl group of the Ala591 side chain, located in the middle of an α helix (res. Glu582-Met603), packs against hydrophobic residues (e.g., Ile483, Phe484) of an opposing partially helical loop (res. Phe476-Asn487).In the variant simulations, Pro591 lacks a free backbone amide group and, therefore, cannot form a hydrogen bond with the backbone carbonyl of Arg587 as Ala591 does in the WT. This notably weakens the α helix integrity and compromises the continuity of the helix. In reality, the effect on the structure during protein folding could be more severe.
c.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>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.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.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.1811C>TS604L
(3D Viewer)
Likely PathogenicGAPUncertain 16-33440863-C-T63.72e-6-14.683Likely Pathogenic0.965Likely PathogenicLikely Pathogenic0.639Likely Pathogenic-0.94Ambiguous0.1-1.24Ambiguous-1.09Ambiguous-0.31Likely Benign-5.97Deleterious1.000Probably Damaging0.991Probably Damaging3.09Benign0.00Affected3.3735-3-24.626.08234.0-49.60.00.10.30.5XXPotentially PathogenicSer604 is located in a short turn between an α helix (res. Glu582-Met603) and a short α helical section (res. Ser606-Phe608). In the WT simulations, the hydroxyl side chain of Ser604 periodically hydrogen bonds with the backbone carbonyl groups of other α helix residues (e.g., Pro600, Met603). Serine weakens the α helix secondary structure, and thus, Ser604 along with Pro605 breaks the α helix, facilitating the turn in the WT structure.In contrast, in the variant simulations, Leu604 forms a few hydrophobic interactions (e.g., Leu607, Phe608). More importantly, the helix end is more stable than with Ser604 in the WT. The residue swap could have a more profound effect on the actual folding process, for example, by preventing the bending at the α helix end, than what the simulations suggest.Moreover, Ser604 directly hydrogen bonds with Ras residues Ser65 and Ala66 in the WT SynGAP-Ras complex. The hydrophobic leucine cannot maintain these interactions with Ras at the GAP-Ras interface. Thus, the effect of the residue swap on the complex formation with the GTPase cannot be fully explored in the solvent-only simulations.
c.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.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.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.1997A>GE666G
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33441256-A-G106.20e-6-12.261Likely Pathogenic0.911Likely PathogenicAmbiguous0.522Likely Pathogenic1.57Ambiguous0.11.46Ambiguous1.52Ambiguous0.93Ambiguous-6.25Deleterious1.000Probably Damaging0.970Probably Damaging3.37Benign0.02Affected3.38280-23.1-72.06173.998.50.00.0-0.70.0XPotentially PathogenicIn the WT simulations, the carboxylate group of Glu666, located on the α-helix (res. Ser641-Glu666), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), such as Lys566, Thr672, and Asn669. In the variant simulations, the carbonyl group of Gly666 occasionally forms hydrogen bonds with Lys566 and Asn669. However, Gly666 lacks a side chain and thus cannot maintain as well-coordinated a hydrogen-bond network as Glu666 in the WT, which may affect the tertiary structure assembly.
c.1998G>CE666D
(3D Viewer)
Likely PathogenicGAPUncertain 1-8.820Likely Pathogenic0.704Likely PathogenicLikely Benign0.197Likely Benign0.88Ambiguous0.00.37Likely Benign0.63Ambiguous1.05Destabilizing-2.69Deleterious0.992Probably Damaging0.603Possibly Damaging3.43Benign0.06Tolerated3.3828320.0-14.03237.216.50.00.0-0.30.1XPotentially PathogenicThe carboxylate group of Glu666, located on the α-helix (res. Ser641-Glu666), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), such as Lys566, Thr672, and Asn669, in the WT simulations. In the variant simulations, the shorter side chain of Asp666 cannot maintain these interactions as efficiently as Glu666 in the WT, resulting in a less coordinated hydrogen-bond network.
c.2003C>TS668F
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-15.047Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.643Likely Pathogenic16.72Destabilizing5.011.07Destabilizing13.90Destabilizing0.00Likely Benign-5.98Deleterious0.999Probably Damaging0.935Probably Damaging3.18Benign0.00Affected3.3828-3-23.660.10250.9-59.6-0.10.10.00.1XXXPotentially PathogenicIn the WT simulations, the hydroxyl side chain of Ser668, located on an α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), forms hydrogen bonds with the backbone carbonyl groups of Leu664, Tyr665, and Glu666, as well as the guanidinium group of Arg573 on a nearby α-helix (res. Arg563-Glu578). In the variant simulations, the side chain of Phe668 cannot maintain the same hydrogen-bond network. Due to its larger size, it moves away to avoid steric hindrance. In the WT simulations, a network of hydrogen bonds between several residues (e.g., Asn669, Lys566, and Glu666) keeps both α-helices and the proceeding loop (res. Asn669-Asp684) tightly connected, but this setup is not present in the variant simulations. Additionally, in the variant simulations, the side chain of Arg573 shifts to form a more stable salt bridge with the carboxylate group of Glu582 instead of hydrogen bonding with Ser668 as in the WT simulations.
c.2014A>GT672A
(3D Viewer)
Likely BenignGAPBenign 16-33441273-A-G31.86e-6-6.524Likely Benign0.109Likely BenignLikely Benign0.046Likely Benign0.51Ambiguous0.31.15Ambiguous0.83Ambiguous0.65Ambiguous-3.20Deleterious0.006Benign0.002Benign3.44Benign0.12Tolerated3.4025102.5-30.03188.542.5-0.10.30.20.0XPotentially PathogenicThe hydroxyl group of Thr672, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop itself, such as Lys566, Glu666, and Asn669. In the variant simulations, Ala672 can only form a hydrogen bond with Lys566 via its backbone carbonyl group. Consequently, it cannot maintain the Lys566-Glu666 salt bridge through hydrogen bonding, leading to a significant disruption of the intricate and stable hydrogen-bond network between the loop and the helices.
c.2015C>AT672K
(3D Viewer)
Likely PathogenicGAPUncertain 1-12.192Likely Pathogenic0.698Likely PathogenicLikely Benign0.065Likely Benign0.20Likely Benign0.51.21Ambiguous0.71Ambiguous0.72Ambiguous-4.31Deleterious0.745Possibly Damaging0.051Benign3.40Benign0.07Tolerated3.40250-1-3.227.07195.17.00.40.70.40.1XXPotentially PathogenicThe hydroxyl group of Thr672, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop itself, such as Lys566, Glu666, and Asn669. In the variant simulations, Lys672 can only form a hydrogen bond with the amino group of the Lys566 side chain via its backbone carbonyl group. Consequently, it cannot maintain the Lys566-Glu666 salt bridge through hydrogen bonding. However, the amino group of Lys periodically forms a salt bridge with the carboxylate group of Glu666, which prevents a drastic disruption of the hydrogen-bond network that keeps the loop close to the helices.
c.2015C>TT672M
(3D Viewer)
GAPConflicting 26-33441274-C-T191.18e-5-9.472Likely Pathogenic0.174Likely BenignLikely Benign0.127Likely Benign0.31Likely Benign0.41.52Ambiguous0.92Ambiguous0.41Likely Benign-4.34Deleterious0.993Probably Damaging0.520Possibly Damaging3.39Benign0.00Affected3.4025-1-12.630.09231.9-52.91.10.10.50.0XXPotentially PathogenicThe hydroxyl group of Thr672, located in an entangled α-α loop connecting the two α-helices (res. Ser641-Glu666 and res. Leu685-Val699), is involved in a highly coordinated hydrogen-bonding network between residues from two α-helices (res. Ser641-Glu666 and res. Arg563-Glu578) and from the α-α loop itself, such as Lys566, Glu666, and Asn669. Met672 can only form a hydrogen bond with the amino group of the Lys566 side chain via its backbone carbonyl group. Nevertheless, the Lys566-Glu666 salt bridge forms intermittently. This is possible because Asn669 keeps the carboxylate group of Glu666 in the vicinity through hydrogen bonding, and the hydrophobic side chain of Met stays mostly rotated away from the salt bridge. Consequently, no drastic disruption of the hydrogen-bond network that keeps the loop close to the helices occurs in the variant simulations.
c.2068T>CS690P
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.568Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.431Likely Benign4.84Destabilizing0.34.40Destabilizing4.62Destabilizing1.42Destabilizing-4.77Deleterious0.998Probably Damaging0.790Possibly Damaging3.44Benign0.01Affected3.42171-1-0.810.04207.515.10.10.0-0.10.2XXPotentially PathogenicThe hydroxyl side chain of Ser690, located in an α-helix (res. Leu696-Leu685), forms a hydrogen bond with the backbone carbonyl group of Ser410 in an anti-parallel β-sheet of the C2 domain (res. Ile411-Ala399). In the variant simulations, the pyrrolidine side chain of Pro690 cannot form hydrogen bonds with the C2 domain residue, resulting in the loss of this inter-domain connection. Additionally, prolines lack a free amide group necessary for hydrogen bonding with the carbonyl group of Gly686, introducing a slight bend in the α-helix and compromising its integrity.
c.2071A>CT691P
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-13.801Likely Pathogenic0.905Likely PathogenicAmbiguous0.214Likely Benign5.04Destabilizing0.46.09Destabilizing5.57Destabilizing1.27Destabilizing-3.43Deleterious1.000Probably Damaging0.952Probably Damaging3.43Benign0.06Tolerated3.43140-1-0.9-3.99188.933.00.10.0-0.60.0XXPotentially PathogenicThe hydroxyl side chain of Thr691, located in an α-helix (res. Leu696-Leu685), can form hydrogen bonds with the backbone carbonyl and the side chain guanidinium group of Arg687. This interaction facilitates the simultaneous formation of salt bridges between Arg687 and Glu688 on the same α-helix. Additionally, Thr691 occasionally interacts with the thioether side chain of Met409 in an anti-parallel β-sheet of the C2 domain (res. Ile411-Ala399), although this interaction is not consistently maintained throughout the WT simulations. In the variant simulations, the pyrrolidine side chain of Pro691 lacks hydrogen bond donors, making a similar setup impossible. Moreover, proline lacks a free amide group necessary for hydrogen bonding with the carbonyl group of Arg687, introducing a slight bend in the α-helix and compromising its integrity.
c.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.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.2105A>GQ702R
(3D Viewer)
GAPUncertain 1-7.894In-Between0.348AmbiguousLikely Benign0.294Likely Benign-0.31Likely Benign0.10.63Ambiguous0.16Likely Benign0.13Likely Benign-3.14Deleterious0.909Possibly Damaging0.889Possibly Damaging3.43Benign0.02Affected3.471011-1.028.06270.3-52.90.00.00.00.1XPotentially PathogenicThe carboxamide side chain of Gln702 is located at the end and outer surface of an α-helix (res. Leu685-Gln702), where it does not directly form hydrogen bonds with any residues in the WT simulations. In the variant simulations, the positively charged guanidinium group of Arg702 forms a salt bridge with the negatively charged carboxylate group of Glu698 on the same helix and/or hydrogen bonds with the backbone carbonyl group of Ala438 on an opposite α-helix (res. Tyr428-Glu436). Consequently, the residue swap could strengthen the tertiary structure assembly, which could have either positive or negative effects on its function.
c.700C>TR234W
(3D Viewer)
Likely PathogenicPHUncertain 16-33435551-C-T31.86e-6-12.625Likely Pathogenic0.947Likely PathogenicAmbiguous0.805Likely Pathogenic0.96Ambiguous0.30.69Ambiguous0.83Ambiguous0.13Likely Benign-5.52Deleterious0.997Probably Damaging0.803Possibly Damaging5.76Benign0.01Affected3.40142-33.630.03262.839.6-0.10.0-0.20.2XPotentially PathogenicThe guanidinium group of Arg234, located in a β-α loop between an anti-parallel β sheet strand (residues Gly227-Phe231) and an α helix (res. Ala236-Val250), forms a salt bridge with the carboxylate group of Glu238 in the α helix. Occasionally, it also bonds with the GAP domain residues Ser678 and Glu680. Thus, the positively charged Arg234 could contribute to the tertiary structure assembly between the PH and GAP domains. In contrast, the indole side chain of Trp234 in the variant is located on the protein surface in the variant simulations and is unable to form any interactions.
c.703T>CS235P
(3D Viewer)
Likely PathogenicPHLikely Pathogenic 1-14.857Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.870Likely Pathogenic4.02Destabilizing0.16.91Destabilizing5.47Destabilizing1.23Destabilizing-4.24Deleterious0.917Possibly Damaging0.446Benign5.47Benign0.01Affected3.40141-1-0.810.04201.517.00.10.0-0.60.0XPotentially PathogenicIn the WT, the hydroxyl group of Ser235, located in a β-α loop between an anti-parallel β sheet strand (res. Gly227-Phe231) and an α helix (residues Ala236-Val250), forms hydrogen bonds with the GAP domain loop residue Glu680 and with the backbone amide groups of Ala237 and Glu238 from the α helix. In the variant simulations, the pyrrolidine ring of Pro235 cannot stabilize the α helix end or maintain tertiary bonding interactions between the PH and GAP domains via hydrogen bonding as effectively as serine.
c.742C>TR248W
(3D Viewer)
Likely PathogenicPHUncertain 1-11.647Likely Pathogenic0.991Likely PathogenicLikely Pathogenic0.699Likely Pathogenic1.17Ambiguous0.3-0.20Likely Benign0.49Likely Benign0.89Ambiguous-6.98Deleterious1.000Probably Damaging0.948Probably Damaging5.62Benign0.00Affected3.41142-33.630.03266.442.30.00.00.30.1XPotentially PathogenicThe guanidinium group of Arg248, located on an α helix (res. Ala236-Val250), forms two very stable salt bridges with Asp255 (from a short α helical section, res. Lys254-Asn256) and Glu244 (from a nearby loop) in the WT simulations. In the variant simulations, the indole group of Trp248 cannot form any salt bridges, which could negatively affect the tertiary structure assembly of the PH domain. Instead, in the variant simulations, the indole ring of Trp248 stacks against Pro252, which makes a turn after the α helix.
c.743G>CR248P
(3D Viewer)
Likely PathogenicPHLikely Pathogenic 1-10.751Likely Pathogenic1.000Likely PathogenicLikely Pathogenic0.848Likely Pathogenic3.09Destabilizing0.68.87Destabilizing5.98Destabilizing1.21Destabilizing-5.97Deleterious0.998Probably Damaging0.878Possibly Damaging5.64Benign0.00Affected3.41140-22.9-59.07223.8126.60.00.0-0.20.1XXPotentially PathogenicThe guanidinium group of Arg248, located on an α helix (residues Ala236-Val250), forms two very stable salt bridges with Asp255 (from a short α helical section, res. Lys254-Asn256) and Glu244 (from a nearby loop) in the WT simulations. In the variant simulations, the pyrrolidine side chain of Pro248 cannot form any salt bridges, which could negatively affect the tertiary structure assembly of the PH domain. Additionally, Pro248 lacks a free amide group needed for hydrogen bonding with the backbone carbonyl group of Asn245, disrupting the continuity of the α helix.
c.762G>CK254N
(3D Viewer)
Likely PathogenicPHUncertain 1-13.306Likely Pathogenic0.999Likely PathogenicLikely Pathogenic0.757Likely Pathogenic0.73Ambiguous0.21.87Ambiguous1.30Ambiguous1.19Destabilizing-4.23Deleterious0.384Benign0.070Benign5.93Benign0.01Affected3.3915100.4-14.07215.3-21.0-1.01.70.20.3XPotentially PathogenicThe amino group of Lys254, located in an α-β loop connecting the PH and C2 domains (res. Lys251-Arg258), forms salt bridges with the carboxylate groups of Glu244 and Asp684. Since the neutral carboxamide group of the Asn254 side chain cannot form salt bridges with acidic residues, the residue swap potentially weakens the tertiary structure assembly and/or influences the loop positioning. Regardless, in both the variant and WT simulations, all hydrogen bonds formed by the residue’s side chain were broken, and the residue rotated outwards. The partially α helical conformation of the loop, which extends to a nearby α helix (res. Met414-Asn426), is dynamic, making it unclear if the mutation affects it.
c.773G>AR258H
(3D Viewer)
C2Benign/Likely benign 36-33437678-G-A106.20e-6-10.533Likely Pathogenic0.525AmbiguousLikely Benign0.830Likely Pathogenic1.60Ambiguous0.61.00Ambiguous1.30Ambiguous1.47Destabilizing-4.06Deleterious1.000Probably Damaging0.991Probably Damaging5.77Benign0.01Affected3.3915201.3-19.05212.581.80.10.0-0.50.2XPotentially PathogenicThe guanidinium group of Arg258, located at the end of an α-β loop connecting the PH domain to the C2 domain (res. Lys251-Arg258), forms hydrogen bonds with the carboxamide groups of Asn727 and Asn729 side chains, as well as with the backbone carbonyl groups of Ala724, Leu725, and Asn727 in the WT simulations. Although the imidazole group of His258 can act as a hydrogen bond donor/acceptor, the swapped residue is unable to maintain an equally well-coordinated hydrogen bond network for linking the C2 and GAP domains in the variant simulations.
c.775C>TR259W
(3D Viewer)
Likely PathogenicC2Uncertain 1-12.186Likely Pathogenic0.985Likely PathogenicLikely Pathogenic0.691Likely Pathogenic1.95Ambiguous0.80.51Ambiguous1.23Ambiguous0.51Ambiguous-7.35Deleterious1.000Probably Damaging0.993Probably Damaging5.76Benign0.00Affected3.39152-33.630.03254.040.00.20.20.20.4XXXPotentially PathogenicThe guanidinium group of Arg259, located at the beginning of an anti-parallel β sheet strand (res. Arg259-Arg272), forms salt bridges with the carboxylate groups of Asp684 at the end of an α helix (res. Ile683-Gln702, GAP domain) and Asp261 on the same β strand. The Arg259 side chain also frequently forms hydrogen bonds with the backbone carbonyl groups of Ser257, Asn256, and Asp255. In the variant simulations, the indole ring of the Trp259 side chain cannot form salt bridges or maintain hydrogen bonding with the carboxylate group of Asp684 or other nearby residues. Notably, the amino group of the Lys254 side chain maintains a salt bridge with Asp684 and Glu244 throughout the variant simulations, while it forms a cation-π bond with the indole ring of Trp259 in the variant. This salt bridge is not maintained in the WT simulations. Additionally, the partially or loosely α helical conformation of a lysine-containing loop (res. Lys251-Ser257), which extends to a nearby α helix (res. Met414-Asn426), could be stabilized due to the residue swap. Moreover, the bulky size of the Trp259 side chain requires nearby residues to adjust their positioning to accommodate the introduced residue, weakening the tertiary structure assembly between the C2, PH, and GAP domains. The residue swap potentially causes more severe effects during protein folding or for the SynGAP-membrane interaction than the solvent-only simulations imply.
c.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.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.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.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.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.886T>GS296A
(3D Viewer)
Likely BenignC2Uncertain 1-6.847Likely Benign0.247Likely BenignLikely Benign0.209Likely Benign0.50Ambiguous0.3-0.26Likely Benign0.12Likely Benign0.35Likely Benign-1.79Neutral0.992Probably Damaging0.987Probably Damaging1.97Pathogenic0.65Tolerated3.4016112.6-16.00182.526.6-0.20.1-0.50.0XPotentially PathogenicThe hydroxyl group of the Ser296 side chain, located in an anti-parallel β sheet strand (res. Met289-Pro298), stably hydrogen bonds with the carboxylate group of Asp330 in a neighboring β strand (res. Ala322-Asp332). The backbone carbonyl group of Ser296 also hydrogen bonds with the guanidinium group of Arg279 in another nearby β strand (res. Arg279-Cys285). In the variant simulations, the methyl group of the Ala296 side chain cannot hydrogen bond with Asp330, causing the carboxylate group positioning to fluctuate more than in the WT simulations.Although the residue swap does not seem to affect the anti-parallel β sheet assembly during the simulations, it is possible that the Ser296-Asp330 hydrogen bond plays a crucial role in maintaining the C2 domain fold. Notably, because Ser296 is located near the membrane interface, the potential effect of the residue swap on the SynGAP-membrane association cannot be addressed by solvent-only simulations.
c.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.899C>TS300F
(3D Viewer)
Likely PathogenicC2Uncertain 1-10.222Likely Pathogenic0.353AmbiguousLikely Benign0.117Likely Benign-0.29Likely Benign0.40.16Likely Benign-0.07Likely Benign0.04Likely Benign-2.66Deleterious0.975Probably Damaging0.596Possibly Damaging1.52Pathogenic0.01Affected3.4719-3-23.660.10233.6-67.6-0.10.00.40.2XXPotentially PathogenicThe hydroxyl group of the Ser300 side chain, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Met289-Pro298, res. Thr305-Asn315), hydrogen bonds with the guanidinium group of Arg299 and the backbone amide group and side chain of Ser302. Thus, in the WT simulations, it contributes to the β hairpin stability. In the variant simulations, the phenol ring of Phe300 cannot form any side chain-related hydrogen bonds, and Arg299 is moved away from its central hairpin loop position.β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Due to its location near the membrane surface, the residue swap could also affect the C2 loop dynamics and SynGAP-membrane association. However, this is beyond the scope of the solvent-only simulations to unravel.
c.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.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.968T>CL323P
(3D Viewer)
Likely PathogenicC2Uncertain 1-12.507Likely Pathogenic0.998Likely PathogenicLikely Pathogenic0.762Likely Pathogenic3.39Destabilizing0.68.46Destabilizing5.93Destabilizing2.20Destabilizing-4.80Deleterious0.999Probably Damaging0.977Probably Damaging0.59Pathogenic0.01Affected4.29398-3-3-5.4-16.04201.968.20.00.10.60.3XPotentially PathogenicThe iso-butyl side chain of Leu323, located at the beginning of an anti-parallel β sheet strand (res. Ala322-Asp330), packs against multiple hydrophobic leucine residues (e.g., Leu264, Leu266, Leu284, Leu286). In contrast, in the variant simulations, the less bulky cyclic five-membered pyrrolidine ring of Pro323 cannot fill the hydrophobic space as effectively as the branched hydrocarbon side chain of leucine. Notably, the backbone amide group of Leu323 forms a hydrogen bond with the backbone carbonyl group of Cys285. Pro323 cannot form this bond due to the absence of the backbone amide group, resulting in partial unfolding of the anti-parallel β sheet end in the variant simulations.
c.968T>GL323R
(3D Viewer)
Likely PathogenicC2Likely Pathogenic 1-14.568Likely Pathogenic0.997Likely PathogenicLikely Pathogenic0.692Likely Pathogenic3.75Destabilizing0.44.47Destabilizing4.11Destabilizing2.15Destabilizing-4.70Deleterious0.999Probably Damaging0.969Probably Damaging0.59Pathogenic0.01Affected3.3922-3-2-8.343.03261.8-61.6-0.40.20.80.2XXXPotentially PathogenicThe iso-butyl side chain of Leu323, located at the beginning of an anti-parallel β sheet strand (res. Ala322-Asp330), packs against multiple hydrophobic leucine residues (e.g., Leu264, Leu266, Leu284, Leu286). In contrast, in the variant simulations, the positively charged guanidinium group of the Arg323 side chain is unsuitable for the hydrophobic niche. Consequently, the side chain either rotates away from the center of the C2 domain or, if it remains within the C2 domain core, it reorients nearby residues to form hydrogen bonds. Regardless, the residue swap extensively disrupts the C2 domain structure.
c.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.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.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.1108G>AG370S
(3D Viewer)
Likely BenignC2Uncertain 16-33438013-G-A159.31e-6-3.533Likely Benign0.081Likely BenignLikely Benign0.282Likely Benign2.83Destabilizing2.01.05Ambiguous1.94Ambiguous-0.02Likely Benign0.47Neutral0.000Benign0.000Benign1.33Pathogenic0.77Tolerated3.421910-0.430.03196.6-49.60.92.2-0.10.4UncertainGly370 is located in the Gly-rich Ω loop (res. Pro364- Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because, the Ω loop is assumed to be directly interacting with the membrane, it is only seen to move arbitrarily throughout the WT solvent simulations. The Ω loop is potentially playing a crucial loop in the SynGAP-membrane complex association, stability and dynamics, regardless, this aspect cannot be addressed through the solvent simulations only. The Ω-loops are known to have a major role in protein functions that requires flexibility and thus, they are rich in glycines, prolines and to a lesser extent, hydrophilic residues to ensure maximum flexibility. Thus, Ser370 in the variant is potentially tolerated in the Ω loop. However, since the effect on the Gly-rich Ω loop dynamics can only be well-studied through the SynGAP-membrane complex, no definite conclusions can be withdrawn.
c.1118G>TG373V
(3D Viewer)
Likely BenignC2Uncertain 16-33438023-G-T65.03e-6-6.062Likely Benign0.112Likely BenignLikely Benign0.428Likely Benign5.32Destabilizing3.20.82Ambiguous3.07Destabilizing0.09Likely Benign-0.98Neutral0.007Benign0.001Benign3.90Benign0.00Affected3.5316-1-34.642.08207.6-68.11.91.1-0.60.1UncertainGly373 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Val373 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on the Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1121C>AS374Y
(3D Viewer)
C2Uncertain 1-7.774In-Between0.344AmbiguousLikely Benign0.310Likely Benign0.71Ambiguous1.20.66Ambiguous0.69Ambiguous-0.02Likely Benign-1.18Neutral0.875Possibly Damaging0.271Benign5.41Benign0.01Affected4.3213-3-2-0.576.10237.3-76.90.50.40.50.3UncertainSer374 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus, large and relatively hydrophobic residues like tyrosine are rarely tolerated. Additionally, the hydroxyl group of Tyr374 frequently forms various hydrogen bonds with other loop residues in the variant simulations. Although no negative structural effects are observed in the variant simulations, Tyr374 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1136C>GS379W
(3D Viewer)
C2Uncertain 16-33438041-C-G-8.898Likely Pathogenic0.388AmbiguousLikely Benign0.520Likely Pathogenic4.32Destabilizing3.43.56Destabilizing3.94Destabilizing0.16Likely Benign-1.02Neutral0.998Probably Damaging0.844Possibly Damaging3.82Benign0.01Affected4.3211-2-3-0.199.14271.3-75.71.41.00.60.5UncertainSer379 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like tryptophan are rarely tolerated. Although no major negative structural effects are observed in the variant simulations, Trp379 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn
c.1136C>TS379L
(3D Viewer)
Likely BenignC2Benign 16-33438041-C-T84.05e-5-5.641Likely Benign0.173Likely BenignLikely Benign0.469Likely Benign0.39Likely Benign0.23.38Destabilizing1.89Ambiguous-0.52Ambiguous-0.85Neutral0.015Benign0.002Benign3.83Benign0.04Affected4.3211-3-24.626.08251.9-48.10.61.10.00.5UncertainSer379 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like leucine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Leu379 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effect on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1142G>TG381V
(3D Viewer)
Likely BenignC2Uncertain 16-33438047-G-T21.25e-6-5.967Likely Benign0.146Likely BenignLikely Benign0.618Likely Pathogenic7.16Destabilizing1.04.10Destabilizing5.63Destabilizing-0.32Likely Benign-0.95Neutral0.386Benign0.157Benign1.32Pathogenic0.10Tolerated4.329-1-34.642.08214.6-68.80.30.7-0.50.3UncertainGly381 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Val381 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effects on Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1150G>AG384S
(3D Viewer)
Likely BenignC2Uncertain 16-33438055-G-A16.22e-7-5.243Likely Benign0.090Likely BenignLikely Benign0.315Likely Benign1.92Ambiguous0.21.66Ambiguous1.79Ambiguous0.19Likely Benign-0.67Neutral0.980Probably Damaging0.968Probably Damaging1.33Pathogenic0.04Affected4.32210-0.430.03202.4-49.80.51.0-0.20.0UncertainGly384 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and so they are rich in glycines, prolines, and, to a lesser extent, small hydrophilic residues to ensure maximum flexibility. Thus, the variant’s Ser384 is potentially tolerated in the Ω loop, although the hydroxyl group of Ser384 forms various hydrogen bonds with several other loop residues in the variant simulations. However, since the effects on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1153T>CS385P
(3D Viewer)
Likely BenignC2Uncertain 16-33438058-T-C-5.431Likely Benign0.123Likely BenignLikely Benign0.385Likely Benign0.91Ambiguous0.6-0.90Ambiguous0.01Likely Benign0.19Likely Benign-0.26Neutral0.676Possibly Damaging0.693Possibly Damaging4.63Benign0.04Affected4.3231-1-0.810.04210.318.51.80.90.30.0UncertainSer385 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and so they are rich in glycine residues, prolines, and, to a lesser extent, small hydrophilic residues to ensure maximum flexibility. Thus, the variant’s Pro385 is potentially tolerated in the Ω loop. However, since the effects on Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1154C>GS385W
(3D Viewer)
C2Benign 16-33438059-C-G-9.353Likely Pathogenic0.362AmbiguousLikely Benign0.373Likely Benign0.53Ambiguous0.20.69Ambiguous0.61Ambiguous0.00Likely Benign-0.84Neutral0.986Probably Damaging0.968Probably Damaging4.63Benign0.00Affected4.323-2-3-0.199.14260.4-71.20.51.30.70.4UncertainSer385 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like tryptophan are rarely tolerated. Although no major negative structural effects are observed in the variant simulations, Trp385 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effects on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.10.1016/j.ajhg.2020.11.011
c.1154C>TS385L
(3D Viewer)
Likely BenignC2Uncertain 26-33438059-C-T94.60e-5-6.018Likely Benign0.167Likely BenignLikely Benign0.304Likely Benign0.16Likely Benign0.10.08Likely Benign0.12Likely Benign-0.26Likely Benign-0.68Neutral0.829Possibly Damaging0.706Possibly Damaging4.63Benign0.01Affected4.323-3-24.626.08244.6-50.10.00.6-0.10.1UncertainSer385 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364, res. Ala399-Ile411). Because the Ω loop is assumed to directly interact with the membrane, it moves arbitrarily throughout the WT solvent simulations. The Ω loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play major roles in protein functions that require flexibility, and thus hydrophobic residues like leucine are rarely tolerated. Although no negative structural effects are observed in the variant simulations, Leu385 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. However, since the effects on Gly-rich Ω loop dynamics can only be studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1160G>TG387V
(3D Viewer)
Likely BenignC2Uncertain 16-33438065-G-T221.37e-5-6.199Likely Benign0.153Likely BenignLikely Benign0.390Likely Benign5.13Destabilizing1.86.44Destabilizing5.79Destabilizing-0.33Likely Benign-0.54Neutral0.069Benign0.077Benign1.32Pathogenic0.01Affected4.323-1-34.642.08207.7-68.4-0.70.8-0.50.1UncertainGly387 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. This loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play significant roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are visualized in the variant’s simulations, Val387 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. Since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1169G>AG390E
(3D Viewer)
C2Uncertain 1-7.913In-Between0.646Likely PathogenicLikely Benign0.575Likely Pathogenic2.61Destabilizing0.94.28Destabilizing3.45Destabilizing0.47Likely Benign-0.87Neutral0.276Benign0.045Benign1.32Pathogenic0.05Affected4.3280-2-3.172.06241.5-108.40.60.5-0.10.1UncertainGly390 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. This loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play significant roles in protein functions that require flexibility, and so they are rich in glycine residues, prolines, and to a lesser extent, small hydrophilic residues to ensure maximum flexibility. Thus, the variant’s Glu390 may not be as well tolerated in the Ω loop. Additionally, the carboxylate group of Glu390 occasionally forms H-bonds with other loop residues in the variant simulations. The interaction between the acidic carboxylate side chain and the acidic membrane lipids may further influence the SynGAP-membrane complex. However, since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1172G>TG391V
(3D Viewer)
Likely BenignC2Likely Benign 16-33438077-G-T31.86e-6-6.642Likely Benign0.133Likely BenignLikely Benign0.595Likely Pathogenic4.23Destabilizing1.34.81Destabilizing4.52Destabilizing-0.11Likely Benign-0.98Neutral0.994Probably Damaging0.887Possibly Damaging1.32Pathogenic0.10Tolerated3.698-1-34.642.08228.6-69.00.00.8-0.50.3UncertainGly387 is located in the Gly-rich Ω loop (res. Pro364-Pro398) between two anti-parallel β sheet strands (res. Thr359-Pro364 and res. Ala399-Ile411). The Ω loop is assumed to directly interact with the membrane, and it is observed to move arbitrarily throughout the WT solvent simulations. This loop potentially plays a crucial role in the SynGAP-membrane complex association, stability, and dynamics. However, this aspect cannot be fully addressed through solvent simulations alone.Ω loops are known to play significant roles in protein functions that require flexibility, and thus hydrophobic residues like valine are rarely tolerated. Although no negative structural effects are visualized in the variant’s simulations, Val391 may exert drastic effects on the SynGAP-membrane complex dynamics and stability. Since the effects on the Gly-rich Ω loop dynamics can only be well studied through the SynGAP-membrane complex, no definite conclusions can be drawn.
c.1322T>CV441A
(3D Viewer)
GAPConflicting 26-33438227-T-C31.86e-6-9.439Likely Pathogenic0.359AmbiguousLikely Benign0.053Likely Benign-0.14Likely Benign0.00.33Likely Benign0.10Likely Benign0.95Ambiguous-2.92Deleterious0.513Possibly Damaging0.214Benign3.44Benign0.93Tolerated3.372900-2.4-28.05195.044.60.00.10.50.0XXUncertainThe iso-propyl side chain of Val441, located on the outer surface of an α helix (res. Asn440-Thr458), does not interact with other residues in the WT simulations. In the variant simulations, the methyl side chain of Ala441 is similarly hydrophobic and does not form any interactions on the outer helix surface. Although the residue swap does not negatively affect the protein structure based on the simulations, it is noteworthy that the residue faces the RasGTPase interface. Thus, the effect of the residue swap on the SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.1441C>TH481Y
(3D Viewer)
Likely PathogenicGAPLikely Benign 16-33438473-C-T169.91e-6-10.910Likely Pathogenic0.565Likely PathogenicLikely Benign0.256Likely Benign-0.53Ambiguous0.1-0.46Likely Benign-0.50Ambiguous0.20Likely Benign-3.32Deleterious0.988Probably Damaging0.979Probably Damaging3.40Benign0.59Tolerated3.3733021.926.03256.5-44.40.00.00.20.2XXUncertainThe imidazole ring of the His481 side chain is located in a short helical structure (res. Glu480-Leu482) within an α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. In the WT simulations, His481 alternately stacks against Arg485, Arg587, and Glu480 without a definite role. In the variant simulations, Tyr481 also alternately stacks with nearby arginine residues, including Arg485, Arg587, and Arg479. The interaction between Tyr481 and Arg479 affects the α-α loop, causing it to fold into a distorted helical structure, an effect that might be more pronounced during protein folding. Finally, the potential effect of the residue swap on SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.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.1456G>AE486K
(3D Viewer)
Likely PathogenicGAPUncertain 1-14.545Likely Pathogenic0.988Likely PathogenicLikely Pathogenic0.435Likely Benign0.06Likely Benign0.10.37Likely Benign0.22Likely Benign0.41Likely Benign-3.58Deleterious1.000Probably Damaging0.988Probably Damaging3.40Benign0.12Tolerated3.373501-0.4-0.94206.852.1-0.30.10.20.0XXUncertainGlu486 is located in an α-α loop connecting the two α-helices (res. Ala461-Phe476 and Leu489-Glu519) at the GAP-Ras interface. It is adjacent to the arginine finger (Arg485) and is expected to closely interact with Ras. The residue swap could affect complex formation with the GTPase and its activation. In the WT simulations, the carboxylate group of Glu486 forms salt bridges with Arg485 and Arg475 on the preceding α-helix (res. Ala461-Phe476). In the variant simulations, Lys486 does not form any specific interactions. Although the amino group of the Lys486 side chain cannot form these salt bridges, no negative effects on the protein structure are observed. Nevertheless, the potential role of Glu486 in SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations, and no definite conclusions can be drawn.
c.1485A>CE495D
(3D Viewer)
Likely PathogenicGAPConflicting 2-3.574Likely Benign0.958Likely PathogenicLikely Pathogenic0.566Likely Pathogenic1.39Ambiguous0.11.03Ambiguous1.21Ambiguous0.98Ambiguous-2.52Deleterious0.998Probably Damaging0.989Probably Damaging-1.41Pathogenic0.17Tolerated3.3735320.0-14.03220.638.80.00.00.10.1XXUncertainGlu495 is located in the α-helix (res. Leu489-Glu519), and its carboxylate group forms salt bridges with the neighboring Lys492 and with Arg596 on an opposing α-helix (res. Glu582-Met603) in the WT simulations. In the variant simulations, the acidic carboxylate side chain of Asp495 can also form salt bridges with both Lys492 and Arg596. However, the shorter side chain of aspartate tends to favor forming a salt bridge with the nearby Arg499 on the same α-helix instead. Asp495 might not maintain the salt bridge with Arg596 on the opposing α-helix as efficiently as Glu495 in the WT, potentially weakening the tertiary structure. Regardless, the potential negative effect is likely to be minor, with no deleterious effects observed on the protein structure during the simulations. However, due to its location at the GAP-Ras interface, the effect of the residue swap on SynGAP-Ras complex formation or GTPase activation cannot be fully addressed using the SynGAP solvent-only simulations.
c.2115G>CK705N
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-9.767Likely Pathogenic0.925Likely PathogenicAmbiguous0.183Likely Benign0.74Ambiguous0.00.37Likely Benign0.56Ambiguous0.44Likely Benign-3.12Deleterious0.996Probably Damaging0.876Possibly Damaging3.37Benign0.02Affected3.4710100.4-14.07221.4-20.20.00.00.00.1XUncertainThe amino side chain of Lys705, located at the end and outer surface of an α-helix (res. Thr704-Gly712), does not form any interactions in the WT simulations. In the variant simulations, the carboxamide side chain of Asn705 briefly forms a salt bridge with Glu706. However, there is no apparent difference between the systems. Due to the model ending abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.1904A>GN635S
(3D Viewer)
GAPConflicting 46-33440956-A-G106.20e-6-9.002Likely Pathogenic0.101Likely BenignLikely Benign0.104Likely Benign0.80Ambiguous0.10.67Ambiguous0.74Ambiguous0.95Ambiguous-4.45Deleterious0.261Benign0.044Benign3.06Benign0.05Affected3.3734112.7-27.03196.030.90.10.0-0.30.2XUncertainIn the WT simulations, the carboxamide side chain of Asn635, located on the outer surface of an α helix (res. Glu617-Asn635), forms hydrogen bonds with Gln631 on the same α helix and with the hydroxyl side chain of Ser590 on an opposing α helix (res. Glu582-Met603).In the variant simulations, the side chain of Ser635 is shorter than asparagine and thus prefers to hydrogen bond with the carbonyl group of Gln631 on the same helix and, to a lesser extent, with Ser590 compared to Asn635 in the WT. Ser635 forms hydrogen bonds with the backbone atoms of the same helix, which may destabilize the helix, although this is not clearly evident in the simulations. The weakening of the hydrogen bond between Ser635 and Ser590 in the variant may also weaken the tertiary structure assembly between the helices.Additionally, Asn635 is at the GTPase interface. However, the implication of the residue swap on the complex formation with the GTPase cannot be investigated using solvent-only simulations.
c.1925A>CK642T
(3D Viewer)
Likely PathogenicGAPLikely Pathogenic 1-12.823Likely Pathogenic0.948Likely PathogenicAmbiguous0.484Likely Benign0.53Ambiguous0.10.30Likely Benign0.42Likely Benign0.28Likely Benign-5.88Deleterious0.872Possibly Damaging0.839Possibly Damaging2.86Benign0.00Affected3.37310-13.2-27.07213.5-8.7-0.30.40.30.2XUncertainThe amino side chain of Lys642, located on the surface of an α helix (res. Ser641-Glu666), is not involved in any interactions in the WT simulations. In the variant simulations, the shorter side chain of Thr642 forms hydrogen bonds with Glu643 and Thr640 on the same α helix.Regardless, Lys642 is positioned directly at the GAP-Ras interface, and in the SynGAP-Ras WT simulations, its amino side chain forms salt bridges with the carboxylate groups of Ras residues Asp33 and Asp38. The shorter Thr642 is more likely to prefer hydrogen bonding with Glu643 and Thr640 on the same α helix, even in the Ras complex. Thus, the effect of the residue swap on the complex formation with the GTPase cannot be explored using solvent-only simulations.
c.2116G>AE706K
(3D Viewer)
GAPUncertain 1-10.519Likely Pathogenic0.833Likely PathogenicAmbiguous0.080Likely Benign1.17Ambiguous0.10.51Ambiguous0.84Ambiguous0.08Likely Benign-1.51Neutral0.345Benign0.028Benign4.15Benign0.52Tolerated3.471001-0.4-0.94187.149.20.00.00.40.1XUncertainThe carboxylate side chain of Glu706, located at the end and outer surface of an α-helix (res. Thr704-Gly712), forms a salt bridge with Lys710 and a hydrogen bond with its own backbone amino group at the helix end in the WT simulations. Although Lys706 is unable to make these transient interactions in the variant simulations, there is no apparent negative effect on the protein structure due to the residue swap. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.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.2147G>AR716Q
(3D Viewer)
GAPConflicting 26-33441612-G-A42.48e-6-8.338Likely Pathogenic0.308Likely BenignLikely Benign0.210Likely Benign-0.01Likely Benign0.00.47Likely Benign0.23Likely Benign0.58Ambiguous-3.14Deleterious1.000Probably Damaging0.990Probably Damaging3.35Benign0.02Affected3.509111.0-28.06250.048.90.00.0-0.50.0XUncertainThe guanidinium group of Arg716, located on the outer surface of an α-helix (res. Leu714-Arg726), forms a salt bridge with the carboxylate group of Asp720. In the variant simulations, the carboxamide group of Gln716 also forms a hydrogen bond with the carboxylate group of Asp720, although this bond is weaker than the Arg716 salt bridge in the WT. Overall, no adverse effects on the protein structure are observed in the simulations. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.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.2168C>TT723I
(3D Viewer)
Likely BenignGAPLikely Benign 16-33441633-C-T21.24e-6-2.591Likely Benign0.120Likely BenignLikely Benign0.045Likely Benign-0.39Likely Benign0.0-0.20Likely Benign-0.30Likely Benign0.26Likely Benign-2.09Neutral0.088Benign0.030Benign3.39Benign0.03Affected3.5080-15.212.05252.3-31.60.00.0-0.20.2XUncertainThe hydroxyl group of Thr723, located on the outer surface of an α-helix (res. Leu714-Arg726), continuously forms hydrogen bonds with the backbone carbonyl of Asn719 in the WT simulations, potentially lowering the stability of the α-helix. In the variant simulations, the sec-butyl side chain of Ile723 cannot form any hydrogen bonds, which, in theory, could increase the helix stability. However, because the model ends abruptly at the C-terminus, no definite conclusions can be drawn based on the simulations.
c.597C>AN199K
(3D Viewer)
PHUncertain 1-8.198Likely Pathogenic0.686Likely PathogenicLikely Benign0.024Likely Benign-0.19Likely Benign0.10.03Likely Benign-0.08Likely Benign0.33Likely Benign-1.48Neutral0.276Benign0.083Benign4.27Benign0.13Tolerated3.47910-0.414.07207.821.5-0.11.50.10.0XUncertainAsn199, located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by a positively charged lysine. On the protein surface, both the carboxamide group of Asn199 and the amino group of Lys199 side chains can form hydrogen bonds with the backbone carbonyl groups of residues (e.g., Ala249) at the end of an α helix (res. Ala236-Lys251). However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.600G>CL200F
(3D Viewer)
PHUncertain 16-33435242-G-C21.24e-6-7.606In-Between0.592Likely PathogenicLikely Benign0.094Likely Benign1.00Ambiguous0.51.45Ambiguous1.23Ambiguous0.43Likely Benign-1.97Neutral0.997Probably Damaging0.916Probably Damaging4.02Benign0.17Tolerated3.46920-1.034.02250.4-15.10.60.20.50.0XUncertainLeu200, a hydrophobic residue located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by another hydrophobic residue, phenylalanine. Both the phenyl group of Phe200 and the branched iso-butyl hydrocarbon sidechain of Leu200 occupy an inward hydrophobic niche (e.g., Leu246, Val222, Phe231) during the simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.603T>AD201E
(3D Viewer)
Likely BenignPHBenign 1-2.640Likely Benign0.406AmbiguousLikely Benign0.165Likely Benign0.42Likely Benign0.21.99Ambiguous1.21Ambiguous0.23Likely Benign-0.69Neutral0.633Possibly Damaging0.108Benign4.30Benign1.00Tolerated3.469320.014.03258.7-24.80.90.1-0.30.2XUncertainAsp201, an acidic residue located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by another acidic residue, glutamate. The carboxylate groups of both Asp201 and Glu201 side chains form hydrogen bonds with the hydroxyl group of Ser221 in the simulations. Due to its shorter side chain, Asp201 can also hydrogen bond with the backbone amide groups of neighboring loop residues Ser204 and Asp203. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.603T>GD201E
(3D Viewer)
Likely BenignPHConflicting 26-33435245-T-G201.24e-5-2.640Likely Benign0.406AmbiguousLikely Benign0.165Likely Benign0.42Likely Benign0.21.99Ambiguous1.21Ambiguous0.23Likely Benign-0.69Neutral0.633Possibly Damaging0.108Benign4.30Benign1.00Tolerated3.469320.014.03258.7-24.80.90.1-0.30.2XUncertainAsp201, an acidic residue located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by another acidic residue, glutamate. The carboxylate groups of both Asp201 and Glu201 side chains form hydrogen bonds with the hydroxyl group of Ser221 in the simulations. Due to its shorter side chain, Asp201 can also hydrogen bond with the backbone amide groups of neighboring loop residues Ser204 and Asp203. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.611C>GS204C
(3D Viewer)
Likely BenignPHUncertain 1-6.613Likely Benign0.127Likely BenignLikely Benign0.148Likely Benign0.65Ambiguous0.4-1.13Ambiguous-0.24Likely Benign0.10Likely Benign-0.64Neutral0.978Probably Damaging0.753Possibly Damaging4.13Benign0.05Affected3.44100-13.316.06223.6-13.80.60.30.00.2XUncertainThe hydroxyl-containing Ser204, located in the N-terminal loop before the first anti-parallel β sheet strand (res. Ile205-Pro208), is replaced by the thiol-containing cysteine. In the WT simulations, Ser204 simultaneously forms hydrogen bonds with the backbone carbonyl of Asp201 and the hydroxyl group of Thr224, helping to stabilize the two anti-parallel β strands (res. Ile205-Lys207 and Cys219-Thr223) at the end of the β sheet. Since the thiol group of cysteine forms weaker hydrogen bonds than the hydroxyl group of serine, Cys204 does not maintain the hydrogen bond network as stably as Ser204 in the variant simulations. However, because the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.662A>TE221V
(3D Viewer)
Likely PathogenicPHLikely Pathogenic 1-14.954Likely Pathogenic0.987Likely PathogenicLikely Pathogenic0.875Likely Pathogenic-0.66Ambiguous0.2-0.89Ambiguous-0.78Ambiguous0.49Likely Benign-5.54Deleterious0.596Possibly Damaging0.203Benign5.86Benign0.00Affected3.4113-2-27.7-29.98234.550.60.00.0-0.40.2XUncertainThe introduced residue Val221 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Unlike the carboxylate group of Glu221, Val221 cannot form hydrogen bonds with Thr223 or a salt bridge with the amino group of the Lys207 side chain. Despite this, the WT simulations containing Glu221 do not show significant differences compared to the variant simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.667A>GT223A
(3D Viewer)
PHUncertain 16-33435518-A-G31.86e-6-7.076In-Between0.316Likely BenignLikely Benign0.574Likely Pathogenic0.30Likely Benign0.10.77Ambiguous0.54Ambiguous0.74Ambiguous-3.36Deleterious0.231Benign0.058Benign5.74Benign0.09Tolerated3.4113102.5-30.03186.444.00.00.00.00.0XXUncertainThe introduced residue Ala223 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Unlike the hydroxyl group of the Thr223 side chain in the WT protein, the methyl side chain of Ala223 cannot form hydrogen bonds with nearby residues Thr228 and Lys207. Without these hydrogen-bonding interactions at the β sheet surface, the secondary structure element becomes unstable and partially unfolds in the variant simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.667A>TT223S
(3D Viewer)
PHConflicting 26-33435518-A-T31.86e-6-7.714In-Between0.410AmbiguousLikely Benign0.535Likely Pathogenic0.26Likely Benign0.10.50Ambiguous0.38Likely Benign0.62Ambiguous-2.86Deleterious0.421Benign0.058Benign5.80Benign0.02Affected3.411311-0.1-14.03200.717.3-0.20.20.00.0XUncertainThe introduced residue Ser223 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Its hydroxyl group forms hydrogen bonds with nearby residues Thr228 and Lys207 in the variant simulations, similar to the hydroxyl group of Thr223 in the WT simulations. These hydrogen-bonding interactions at the β sheet surface contribute to the stability of the secondary structure element and may prevent it from unfolding. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.670A>GT224A
(3D Viewer)
PHUncertain 36-33435521-A-G21.24e-6-7.379In-Between0.651Likely PathogenicLikely Benign0.464Likely Benign0.33Likely Benign0.11.05Ambiguous0.69Ambiguous0.91Ambiguous-2.96Deleterious0.243Benign0.079Benign5.57Benign0.57Tolerated3.4113102.5-30.03169.041.4-0.51.1-0.40.0XXUncertainThe introduced residue Ala224 is located on the outer surface of an anti-parallel β sheet strand (res. Cys219-Thr224). Unlike the hydroxyl group of the Thr224 side chain in the WT model, the methyl side chain of Ala224 cannot form hydrogen bonds with nearby residues Ser204, Ser226, and Gly227. Without these hydrogen-bonding interactions at the β sheet surface, the secondary structure element becomes unstable and unfolds during the variant simulations. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.680G>AG227E
(3D Viewer)
Likely PathogenicPHConflicting 26-33435531-G-A31.86e-6-9.186Likely Pathogenic0.996Likely PathogenicLikely Pathogenic0.792Likely Pathogenic2.56Destabilizing0.45.36Destabilizing3.96Destabilizing0.94Ambiguous-6.49Deleterious0.906Possibly Damaging0.360Benign5.72Benign0.01Affected3.43120-2-3.172.06237.7-112.10.10.30.00.3XXUncertainThe introduced residue Glu227 is located in a β hairpin loop connecting two anti-parallel β sheet strands (res. Cys219-Thr224 and Thr228-Ala232). In the variant simulations, the carboxylate group of Glu227 frequently forms a salt bridge with the amino group of the neighboring residue Lys229. Despite this interaction, the integrity of the secondary structure element is not compromised. However, the β hairpins are potential nucleation sites during the initial stages of protein folding. Additionally, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.694G>AA232T
(3D Viewer)
PHBenign 16-33435545-G-A16.20e-7-7.655In-Between0.874Likely PathogenicAmbiguous0.469Likely Benign0.47Likely Benign0.1-0.04Likely Benign0.22Likely Benign0.61Ambiguous-1.42Neutral0.608Possibly Damaging0.240Benign5.80Benign0.09Tolerated3.401410-2.530.03210.8-42.00.50.10.40.5XUncertainThe hydroxyl group of Thr232, located at the end of an anti-parallel β sheet strand (res. Thr228-Ala232), forms hydrogen bonds with nearby residues Glu217, Cys233, and Cys219 in the variant simulations. These hydrogen-bonding interactions at the β sheet surface contribute to the stability of the secondary structure element and prevent it from unfolding. The new hydrogen bond interactions may be more favorable for structural stability than the steric interactions of the methyl side chain of Ala with the side chains of Gln216 and Cys219 in the WT. However, since the model ends abruptly at the N-terminus, no definite conclusions can be drawn from the simulations.
c.815G>AR272Q
(3D Viewer)
C2Uncertain 26-33437720-G-A148.67e-6-9.559Likely Pathogenic0.286Likely BenignLikely Benign0.321Likely Benign0.73Ambiguous0.10.15Likely Benign0.44Likely Benign1.00Destabilizing-1.81Neutral0.999Probably Damaging0.994Probably Damaging1.88Pathogenic0.03Affected3.3819111.0-28.06255.752.90.00.0-0.20.1XUncertainThe guanidinium group of Arg272, located at the end of an anti-parallel β sheet strand (res. Arg259-Arg272), is stably maintained in an upright and outward position via stacking with the indole ring of the Trp362 side chain in another β strand (res. Thr359-Pro364). In the WT simulations, Arg272 forms hydrogen bonds with the glycine-rich Ω loop residues (res. Val365-Pro398, e.g., Gly380) and creates a salt bridge with the carboxylate group of the Asp304 side chain.In the variant simulations, the carboxamide group of the Gln272 side chain does not stack with the indole ring of Trp362 as stably as the guanidinium group of Arg272 in the WT. Consequently, the Gln272 side chain is freer to interact with the loop residues than Arg272, potentially negatively affecting the dynamic SynGAP-membrane association. Additionally, Arg272 faces the RasGTPase interface, so the residue swap could impact the SynGAP-Ras complex formation and GTPase activation.
c.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.901G>AA301T
(3D Viewer)
Likely BenignC2Uncertain 56-33437806-G-A21.24e-6-3.448Likely Benign0.070Likely BenignLikely Benign0.150Likely Benign0.36Likely Benign0.2-0.33Likely Benign0.02Likely Benign0.03Likely Benign-0.25Neutral0.997Probably Damaging0.989Probably Damaging4.15Benign0.22Tolerated4.321410-2.530.03219.8-42.8-0.10.0-0.50.2UncertainThe methyl group of Ala301, located in a β hairpin loop linking two anti-parallel β sheet strands (res. Met289-Pro298, res. Thr305-Asn315), points outward from the β hairpin loop, and its backbone atoms do not participate in the loop formation in the WT simulations. In the variant simulations, the hydroxyl group of the Thr301 side chain also mostly points outward; however, the guanidinium group of Arg299 is moved away from its central hairpin loop position.β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Due to its location near the membrane surface, the residue swap could also affect the C2 loop dynamics and SynGAP-membrane association. However, this is beyond the scope of the solvent-only simulations to unravel.
c.913A>GT305A
(3D Viewer)
Likely BenignC2Conflicting 26-33437818-A-G138.05e-6-4.307Likely Benign0.078Likely BenignLikely Benign0.144Likely Benign1.30Ambiguous0.61.55Ambiguous1.43Ambiguous0.77Ambiguous-2.10Neutral0.939Possibly Damaging0.645Possibly Damaging1.76Pathogenic0.12Tolerated3.4020102.5-30.03177.943.5-0.20.10.40.0UncertainThe hydroxyl group of Thr305, located at the beginning of an anti-parallel β strand (res. Thr305-Asn315), hydrogen bonds with the carboxylate groups of Glu270 and Asp304 in the anti-parallel β strand and the adjacent β hairpin loop, respectively. In the variant simulations, the methyl group of the Ala305 side chain cannot hydrogen bond with either of the acidic residues, which could weaken the integrity of the tertiary structure and the β hairpin loop. Indeed, the guanidinium group of Arg299 does not acquire its central hairpin loop position due to the residue swap.β hairpins are potential nucleation sites during the initial stages of protein folding, so even minor changes in them could be significant. Due to its location near the membrane surface, the residue swap could also affect the C2 loop dynamics and SynGAP-membrane association. However, this is beyond the scope of the solvent-only simulations to unravel.
c.986G>AR329H
(3D Viewer)
Likely PathogenicC2Uncertain 16-33437891-G-A21.24e-6-10.154Likely Pathogenic0.769Likely PathogenicLikely Benign0.155Likely Benign2.53Destabilizing0.70.71Ambiguous1.62Ambiguous0.82Ambiguous-3.17Deleterious0.995Probably Damaging0.778Possibly Damaging4.04Benign0.05Affected3.4115201.3-19.05220.481.40.10.10.20.3UncertainThe guanidinium group of Arg329, located at the end of an anti-parallel β sheet strand (res. Ala322-Asp330), faces the negatively charged lipid bilayer surface. While the residue swap does not cause any apparent negative effects on the protein structure in the variant simulations, it could adversely affect the SynGAP-membrane association in reality. The positively charged Arg329 side chain forms hydrogen bonds with other loop residues (e.g., Ser371, Asp338) that are expected to dynamically interact with the membrane head group region. However, this phenomenon is beyond the scope of the solvent-only simulations to unravel. Notably, histidine can also be double protonated and positively charged, but this alternative protonation state was not considered in the variant simulations.

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