GYS2 (P54840) variants and mutations
GYS2 (also known as P54840) is a human protein-coding gene encoding a glycogen [starch] synthase, liver protein. The liver form of glycogen synthase, which adds glucose units during glycogen production. Variants cause hepatic glycogen storage disease type 0. This analysis covers 1,088 GYS2 variants and mutations. Of these, 100% have computational variant effect predictions. Disease context includes glycogen storage disorder due to hepatic glycogen synthase deficiency, disorder of glycogen metabolism, and glycogen storage disease XV. Example GYS2 variants include L2F, L2I, and R3Q.
Variant analysis overview
- Gene: GYS2
- Protein: P54840
- UniProt accession: P54840
- Organism: Homo sapiens
- Variants analyzed: 1088
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 925 unspecified-consequence records; 1 stop lost; 97 synonymous variants; 136 missense variants; 23 frameshift variants; 9 stop-gained variants; 4 in-frame deletions; 2 splice-region variants; 1 substitution
- Prediction scores: 1,099 variants have prediction scores (101% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: glycogen storage disorder due to hepatic glycogen synthase deficiency, disorder of glycogen metabolism, glycogen storage disease XV, infectious disease, hereditary disease, diabetes mellitus, type 2 diabetes mellitus, schizophrenia, ischemic stroke, 3-hydroxy-3-methylglutaryl-CoA synthase deficiency, intrahepatic cholangiocarcinoma, neoplasm.
Protein structure and variant hotspots
- Protein features: 17 binding sites; 9 post-translational modification sites.
- PTM context: 17 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Diseases linked to GYS2
Notable GYS2 variants
Examples include L2F, L2I, R3Q, G4D, R5*, R5G, R5Q, S6C. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- L2F (p.Leu2Phe), gnomAD rs1223813221, ESM-1b 0.00, AlphaMissense 0.07, Uncertain significance, Inborn genetic diseases
- L2I (p.Leu2Ile), gnomAD rs1223813221, REVEL 0.05, ESM-1b 0.00
- R3Q (p.Arg3Gln), rs750090305, NCI-TCGA Cosmic COSV5392, ExAC rs750090305, gnomAD rs750090305, REVEL 0.13, ESM-1b 0.76, Variant assessed as somatic; moderate impact.
- G4D (p.Gly4Asp), ExAC rs764394742, gnomAD rs764394742, REVEL 0.19, ESM-1b 0.00
- R5* (p.Arg5Ter), ExAC rs775874593, TOPMed rs775874593, gnomAD rs775874593, CADD 26.40, Pathogenic
- R5G (p.Arg5Gly), ExAC rs775874593, TOPMed rs775874593, gnomAD rs775874593, REVEL 0.35, ESM-1b 1.00, Pathogenic
- R5Q (p.Arg5Gln), 1000Genomes rs535288005, ExAC rs535288005, TOPMed rs535288005, gnomAD rs535288005, REVEL 0.20, ESM-1b 1.00
- S6C (p.Ser6Cys), rs141614479, ESP rs141614479, ExAC rs141614479, TOPMed rs141614479, REVEL 0.25, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- S11F (p.Ser11Phe), gnomAD rs1401317610, REVEL 0.36, ESM-1b 1.00
- S11P (p.Ser11Pro), TOPMed rs1179574081, gnomAD rs1179574081, REVEL 0.36, ESM-1b 1.00
- L12P (p.Leu12Pro), ExAC rs747176029, gnomAD rs747176029, REVEL 0.47, ESM-1b 1.00
- G13D (p.Gly13Asp), ExAC rs772461189, gnomAD rs772461189, REVEL 0.04, ESM-1b 0.00
- L15F (p.Leu15Phe), Ensembl rs200917760, REVEL 0.17, ESM-1b 0.23
- L15P (p.Leu15Pro), gnomAD rs1944786295, REVEL 0.48, ESM-1b 1.00
- P16A (p.Pro16Ala), ExAC rs747932329, TOPMed rs747932329, gnomAD rs747932329, REVEL 0.20, ESM-1b 0.33
- P16L (p.Pro16Leu), gnomAD rs1944786206, REVEL 0.21, ESM-1b 1.00
- P16T (p.Pro16Thr), ExAC rs747932329, TOPMed rs747932329, gnomAD rs747932329, REVEL 0.23, ESM-1b 0.43
- Q17H (p.Gln17His), ExAC rs749251980, TOPMed rs749251980, gnomAD rs749251980, REVEL 0.04, ESM-1b 0.00
- Q17R (p.Gln17Arg), rs376935348, ClinGen CA6480290, ClinVar RCV000824324, ClinVar RCV006367420, REVEL 0.02, ESM-1b 0.00, Conflicting interpretations, Glycogen storage disorder due to hepatic glycogen synthase deficiency; Inborn ge
- V20I (p.Val20Ile), TOPMed rs1944786001, gnomAD rs1944786001, REVEL 0.07, ESM-1b 0.00
- E21K (p.Glu21Lys), NCI-TCGA Cosmic COSV5392, TOPMed rs1409001505, gnomAD rs1409001505, REVEL 0.04, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- E21Q (p.Glu21Gln), rs1409001505, NCI-TCGA Cosmic COSV5392, TOPMed rs1409001505, REVEL 0.04, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- E22D (p.Glu22Asp), ExAC rs755644570, TOPMed rs755644570, gnomAD rs755644570, REVEL 0.06, ESM-1b 0.00
- L23F (p.Leu23Phe), rs750040511, NCI-TCGA Cosmic COSV5392, ExAC rs750040511, gnomAD rs750040511, REVEL 0.09, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- L23H (p.Leu23His), Ensembl rs1944785541, ESM-1b 0.00, AlphaMissense 0.49
- P24T (p.Pro24Thr), gnomAD rs1197384808, REVEL 0.17, ESM-1b 0.89
- V25A (p.Val25Ala), TOPMed rs1418654756, gnomAD rs1418654756, REVEL 0.11, ESM-1b 0.00
- E26G (p.Glu26Gly), ExAC rs767128558, TOPMed rs767128558, gnomAD rs767128558, REVEL 0.09, ESM-1b 0.83
- E26K (p.Glu26Lys), TOPMed rs1944785432, ESM-1b 0.00, AlphaMissense 0.12
- E27D (p.Glu27Asp), TOPMed rs1470327566, REVEL 0.06, ESM-1b 0.00
- L28S (p.Leu28Ser), TOPMed rs1944785258, gnomAD rs1944785258, REVEL 0.27, ESM-1b 0.00
- L29P (p.Leu29Pro), rs1242569336, ClinGen CA384295769, ClinVar RCV004388763, TOPMed rs1242569336, REVEL 0.39, ESM-1b 0.51, Uncertain significance, Inborn genetic diseases; not provided
- L30F (p.Leu30Phe), TOPMed rs1944785094, gnomAD rs1944785094, REVEL 0.22, ESM-1b 1.00
- E32D (p.Glu32Asp), ExAC rs756956421, TOPMed rs756956421, gnomAD rs756956421, REVEL 0.62, ESM-1b 1.00, Conflicting interpretations, GYS2-related disorders; Glycogen storage disorder due to hepatic glycogen syntha
- V33A (p.Val33Ala), rs753050580, ClinGen CA6480283, ClinVar RCV004388764, ExAC rs753050580, REVEL 0.33, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases
- W35* (p.Trp35Ter), Ensembl rs1944784944, CADD 37.00
- W35R (p.Trp35Arg), gnomAD rs1944784970, REVEL 0.67, ESM-1b 1.00
- W35S (p.Trp35Ser), Ensembl rs1944784944, ESM-1b 1.00, AlphaMissense 0.89
- E36K (p.Glu36Lys), Ensembl rs1591816790, REVEL 0.74, ESM-1b 1.00
- V37L (p.Val37Leu), Ensembl rs1944784891, ESM-1b 1.00, AlphaMissense 0.98
- N39D (p.Asn39Asp), ExAC rs765703616, gnomAD rs765703616, REVEL 0.54, ESM-1b 1.00
- N39K (p.Asn39Lys), rs777214550, ClinGen CA234079668, ClinVar RCV001928151, ExAC rs777214550, REVEL 0.41, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- N39S (p.Asn39Ser), rs121918423, ClinGen CA126173, ClinVar RCV000017432, UniProt VAR 007860, REVEL 0.57, ESM-1b 1.00, Pathogenic/Likely pathogenic, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- G42E (p.Gly42Glu), rs1336397751, gnomAD rs1336397751, REVEL 0.86, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- G43T (p.Gly43Thr), NCI-TCGA TCGA novel, MetaLR 0.59, MetaSVM 0.35, Variant assessed as somatic; moderate impact.
- I44V (p.Ile44Val), Ensembl rs2136913531, REVEL 0.52, ESM-1b 1.00
- Y45C (p.Tyr45Cys), ExAC rs780740780, gnomAD rs780740780, REVEL 0.34, ESM-1b 1.00
- Y45F (p.Tyr45Phe), ExAC rs780740780, gnomAD rs780740780, REVEL 0.39, ESM-1b 1.00
- I48T (p.Ile48Thr), ExAC rs756901644, TOPMed rs756901644, gnomAD rs756901644, REVEL 0.79, ESM-1b 1.00
- I48V (p.Ile48Val), TOPMed rs199980772, gnomAD rs199980772, REVEL 0.22, ESM-1b 0.00
- Q49* (p.Gln49Ter), TOPMed rs1038631937, CADD 39.00
- Q49H (p.Gln49His), TOPMed rs1229680625, gnomAD rs1229680625, REVEL 0.35, ESM-1b 1.00
- T50I (p.Thr50Ile), ExAC rs751232960, gnomAD rs751232960, REVEL 0.48, ESM-1b 1.00
- A52S (p.Ala52Ser), TOPMed rs886049162, gnomAD rs886049162, REVEL 0.59, ESM-1b 1.00, Uncertain significance
- A52T (p.Ala52Thr), rs886049162, ClinGen CA10640673, ClinVar RCV000352357, TOPMed rs886049162, REVEL 0.76, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- T54K (p.Thr54Lys), TOPMed rs1944496636, ESM-1b 0.44, AlphaMissense 0.51
- T55A (p.Thr55Ala), gnomAD rs1378899165, REVEL 0.48, ESM-1b 1.00
- W59* (p.Trp59Ter), ExAC rs201868350, TOPMed rs201868350, gnomAD rs201868350, CADD 37.00, Likely pathogenic
- W59R (p.Trp59Arg), Ensembl rs1944496482, REVEL 0.61, ESM-1b 1.00
- W59S (p.Trp59Ser), ExAC rs201868350, TOPMed rs201868350, gnomAD rs201868350, REVEL 0.46, ESM-1b 1.00, Likely pathogenic
- G60T (p.Gly60Thr), NCI-TCGA TCGA novel, MetaLR 0.33, MetaSVM -0.52, Variant assessed as somatic; moderate impact.
- G60E (p.Gly60Glu), Ensembl rs1944496399, ESM-1b 1.00, AlphaMissense 0.45
- E61D (p.Glu61Asp), ExAC rs750525944, TOPMed rs750525944, gnomAD rs750525944, NCI-TCGA Cosmic COSV5392, REVEL 0.06, ESM-1b 0.00, Likely benign, Inborn genetic diseases
- N62K (p.Asn62Lys), TOPMed rs1290083695, REVEL 0.22, ESM-1b 0.00
- N62T (p.Asn62Thr), TOPMed rs1944496286, ESM-1b 1.00, AlphaMissense 0.54
- N62Y (p.Asn62Tyr), Ensembl rs1565607596, REVEL 0.53, ESM-1b 1.00
- Y63C (p.Tyr63Cys), TOPMed rs1450570025, gnomAD rs1450570025, REVEL 0.84, ESM-1b 1.00
- F64C (p.Phe64Cys), Ensembl rs1591803486, ESM-1b 0.00, AlphaMissense 0.33
- F64L (p.Phe64Leu), TOPMed rs1218654364, gnomAD rs1218654364, REVEL 0.16, ESM-1b 0.43
- L65P (p.Leu65Pro), Ensembl rs1944496073, ESM-1b 1.00, AlphaMissense 0.99
- I66T (p.Ile66Thr), ExAC rs762069552, gnomAD rs762069552, REVEL 0.46, ESM-1b 1.00
- I66V (p.Ile66Val), ExAC rs767709466, gnomAD rs767709466, REVEL 0.07, ESM-1b 0.00
- G67T (p.Gly67Thr), NCI-TCGA Cosmic COSV5392, Variant assessed as somatic; high impact.
- Y69* (p.Tyr69Ter), ExAC rs774656122, gnomAD rs774656122, CADD 35.00
- H72R (p.His72Arg), rs574787003, ClinGen CA6480252, ClinVar RCV001115118, ClinVar RCV004978025, REVEL 0.08, ESM-1b 0.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency; Inborn ge
- N73S (p.Asn73Ser), 1000Genomes rs554881012, ExAC rs554881012, gnomAD rs554881012, REVEL 0.27, ESM-1b 0.00
- M74L (p.Met74Leu), TOPMed rs1243790256, ESM-1b 0.00, AlphaMissense 0.19
- T76G (p.Thr76Gly), NCI-TCGA Cosmic COSV5392, REVEL 0.83, MetaLR 0.60, Variant assessed as somatic; moderate impact.
- C81T (p.Cys81Thr), NCI-TCGA Cosmic COSV5392, MetaLR 0.17, MetaSVM -0.91, Variant assessed as somatic; moderate impact.
- C81G (p.Cys81Gly), 1000Genomes rs146200724, ExAC rs146200724, TOPMed rs146200724, gnomAD rs146200724, REVEL 0.24, ESM-1b 1.00, Uncertain significance
- C81S (p.Cys81Ser), rs146200724, ClinGen CA6480249, ClinVar RCV001893537, 1000Genomes rs146200724, REVEL 0.09, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- C81Y (p.Cys81Tyr), Ensembl rs1944495631, REVEL 0.16, ESM-1b 1.00
- C81A (p.Cys81Ala), NCI-TCGA TCGA novel, MetaLR 0.11, MetaSVM -1.01, Variant assessed as somatic; moderate impact.
- E82K (p.Glu82Lys), NCI-TCGA Cosmic COSV5392, TOPMed rs1944495595, ESM-1b 1.00, AlphaMissense 0.17, Variant assessed as somatic; moderate impact.
- P83L (p.Pro83Leu), ExAC rs745875719, TOPMed rs745875719, gnomAD rs745875719, REVEL 0.39, ESM-1b 1.00
- P83S (p.Pro83Ser), gnomAD rs1345027888, REVEL 0.25, ESM-1b 1.00
- V84I (p.Val84Ile), TOPMed rs1359210515, gnomAD rs1359210515, REVEL 0.08, ESM-1b 0.00
- N85S (p.Asn85Ser), gnomAD rs1318026904, REVEL 0.08, ESM-1b 0.00
- D86G (p.Asp86Gly), rs1944495395, ClinGen CA384139006, ClinVar RCV002004387, ClinVar RCV006368108, REVEL 0.09, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Glycogen storage disorder due to hepatic glycogen synth
- D86N (p.Asp86Asn), rs1401658816, ClinGen CA384139016, ClinVar RCV004388758, NCI-TCGA TCGA novel, REVEL 0.23, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases
- D86Y (p.Asp86Tyr), TOPMed rs1401658816, gnomAD rs1401658816, REVEL 0.24, ESM-1b 0.00, Uncertain significance
- A87S (p.Ala87Ser), gnomAD rs1409635734, REVEL 0.19, ESM-1b 0.00
- A87V (p.Ala87Val), NCI-TCGA Cosmic COSV5392, TOPMed rs1944495238, REVEL 0.09, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- V88I (p.Val88Ile), TOPMed rs1050896862, REVEL 0.08, ESM-1b 0.00
- R89* (p.Arg89Ter), ExAC rs770445648, TOPMed rs770445648, gnomAD rs770445648
- D93E (p.Asp93Glu), rs779704436, ClinGen CA321416, ClinVar RCV000196989, ExAC rs779704436, REVEL 0.16, ESM-1b 0.00, Likely benign, not specified
- A94S (p.Ala94Ser), 1000Genomes rs34225615, ESP rs34225615, ExAC rs34225615, TOPMed rs34225615, REVEL 0.20, ESM-1b 0.00, Benign
- A94T (p.Ala94Thr), rs34225615, ClinGen CA291139, ClinVar RCV000125330, ClinVar RCV000675357, REVEL 0.17, ESM-1b 0.00, Benign, not specified; not provided; Glycogen storage disorder due to hepatic glycogen s
- M95R (p.Met95Arg), Ensembl rs1944494905, REVEL 0.77, ESM-1b 1.00
- M95V (p.Met95Val), rs2540540835, ClinGen CA384138912, ClinVar RCV002646030, REVEL 0.38, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- N96H (p.Asn96His), Ensembl rs1944494873, REVEL 0.20, ESM-1b 0.00
- K97E (p.Lys97Glu), rs886049161, ClinGen CA10632436, ClinVar RCV000386889, Ensembl rs886049161, ESM-1b 0.00, AlphaMissense 0.13, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- K97M (p.Lys97Met), TOPMed rs1363490595, gnomAD rs1363490595, REVEL 0.15, ESM-1b 0.00
- H98R (p.His98Arg), TOPMed rs1479342425, gnomAD rs1479342425, REVEL 0.16, ESM-1b 0.00
- G99R (p.Gly99Arg), ExAC rs754215144, gnomAD rs754215144, REVEL 0.87, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases
- C100F (p.Cys100Phe), 1000Genomes rs144077289, ESP rs144077289, ExAC rs144077289, TOPMed rs144077289, REVEL 0.57, ESM-1b 0.00, Conflicting interpretations, not provided; Glycogen storage disorder due to hepatic glycogen synthase deficie
- C100Y (p.Cys100Tyr), rs144077289, ClinGen CA320440, ClinVar RCV000196043, ClinVar RCV002517222, REVEL 0.55, ESM-1b 0.00, Uncertain significance, not provided; Glycogen storage disorder due to hepatic glycogen synthase deficie
- C100T (p.Cys100Thr), NCI-TCGA Cosmic COSV9968, Variant assessed as somatic; moderate impact.
- Q101* (p.Gln101Ter), Ensembl rs1944494504, CADD 46.00
- V102G (p.Val102Gly), Ensembl rs1591800840, ESM-1b 1.00, AlphaMissense 0.75
- V102M (p.Val102Met), Ensembl rs1944443326, REVEL 0.70, ESM-1b 0.87
- H103R (p.His103Arg), rs376308462, ClinGen CA6480224, ClinVar RCV003055557, ESP rs376308462, REVEL 0.09, ESM-1b 0.03, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- W107* (p.Trp107Ter), TOPMed rs1364491647, gnomAD rs1364491647, CADD 39.00
- W107R (p.Trp107Arg), gnomAD rs1215714641, REVEL 0.90, ESM-1b 1.00
- G111R (p.Gly111Arg), rs1284586998, NCI-TCGA Cosmic COSV5392, TOPMed rs1284586998, gnomAD rs1284586998, REVEL 0.83, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- P113L (p.Pro113Leu), Ensembl rs1565605986, REVEL 0.87, ESM-1b 1.00
- P113S (p.Pro113Ser), Ensembl rs890971908, REVEL 0.87, ESM-1b 1.00
- Y114H (p.Tyr114His), ExAC rs757754937, TOPMed rs757754937, gnomAD rs757754937, REVEL 0.25, ESM-1b 0.00
- V115A (p.Val115Ala), TOPMed rs1944442668, REVEL 0.73, ESM-1b 0.00
- V115M (p.Val115Met), ExAC rs764149075, gnomAD rs764149075, REVEL 0.72, ESM-1b 1.00
- V116A (p.Val116Ala), ExAC rs752934036, gnomAD rs752934036, ESM-1b 1.00, AlphaMissense 0.75
- V116G (p.Val116Gly), ExAC rs752934036, gnomAD rs752934036, REVEL 0.73, ESM-1b 1.00
- V116I (p.Val116Ile), rs758582300, ClinGen CA6480218, ClinVar RCV002817658, ExAC rs758582300, REVEL 0.08, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases
- V116L (p.Val116Leu), ExAC rs758582300, TOPMed rs758582300, gnomAD rs758582300, REVEL 0.10, ESM-1b 1.00, Uncertain significance
- L117P (p.Leu117Pro), Ensembl rs2136906420, REVEL 0.90, ESM-1b 1.00
- F118L (p.Phe118Leu), Ensembl rs1944442501, ESM-1b 0.52, AlphaMissense 0.64
- F118S (p.Phe118Ser), ExAC rs764967152, TOPMed rs764967152, gnomAD rs764967152, REVEL 0.84, ESM-1b 1.00
- D119N (p.Asp119Asn), ExAC rs759292321, gnomAD rs759292321, REVEL 0.54, ESM-1b 1.00
- I120K (p.Ile120Lys), TOPMed rs1227967058, ESM-1b 1.00, AlphaMissense 0.89
- I120M (p.Ile120Met), ESP rs371292004, TOPMed rs371292004, gnomAD rs371292004, ESM-1b 0.80, AlphaMissense 0.17
- G121T (p.Gly121Thr), NCI-TCGA Cosmic COSV9967, REVEL 0.28, ESM-1b 0.00, Variant assessed as somatic; moderate impact.
- Y122C (p.Tyr122Cys), TOPMed rs1944442366, REVEL 0.28, ESM-1b 0.00
- A124G (p.Ala124Gly), NCI-TCGA Cosmic COSV9968, MetaLR 0.50, MetaSVM 0.10, Variant assessed as somatic; moderate impact.
- W125C (p.Trp125Cys), ExAC rs766324299, TOPMed rs766324299, gnomAD rs766324299, REVEL 0.53, ESM-1b 1.00
- W125R (p.Trp125Arg), Ensembl rs1944442292, REVEL 0.53, ESM-1b 1.00
- L127P (p.Leu127Pro), ExAC rs760594068, gnomAD rs760594068, REVEL 0.88, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- R129G (p.Arg129Gly), TOPMed rs1217435046, ESM-1b 1.00, AlphaMissense 0.31
- R129K (p.Arg129Lys), Ensembl rs1565605946, REVEL 0.07, ESM-1b 0.00
- R129W (p.Arg129Trp), TOPMed rs1217435046, ESM-1b 1.00, AlphaMissense 0.34
- W130* (p.Trp130Ter), gnomAD rs1205332809, CADD 37.00
- K131N (p.Lys131Asn), ESP rs373285780, TOPMed rs373285780, gnomAD rs373285780, REVEL 0.59, ESM-1b 1.00
- G132A (p.Gly132Ala), 1000Genomes rs541099681, ExAC rs541099681, TOPMed rs541099681, gnomAD rs541099681, ESM-1b 1.00, AlphaMissense 0.18, Likely benign
- G132C (p.Gly132Cys), TOPMed rs1944441887, gnomAD rs1944441887, REVEL 0.56, ESM-1b 1.00
- G132D (p.Gly132Asp), rs541099681, ClinGen CA323426, ClinVar RCV000198897, 1000Genomes rs541099681, REVEL 0.43, ESM-1b 1.00, Likely benign, not specified
- D133A (p.Asp133Ala), Ensembl rs1591800710, ESM-1b 1.00, AlphaMissense 0.47
- D133N (p.Asp133Asn), ExAC rs774186653, TOPMed rs774186653, gnomAD rs774186653, REVEL 0.25, ESM-1b 1.00
- L134I (p.Leu134Ile), ExAC rs746184836, gnomAD rs746184836, REVEL 0.23, ESM-1b 1.00
- A137E (p.Ala137Glu), ExAC rs781699106, gnomAD rs781699106, ESM-1b 1.00, AlphaMissense 0.36
- A137T (p.Ala137Thr), TOPMed rs1179811379, gnomAD rs1179811379, REVEL 0.05, ESM-1b 0.00
- A137V (p.Ala137Val), ExAC rs781699106, gnomAD rs781699106, REVEL 0.05, ESM-1b 0.00
- C138G (p.Cys138Gly), NCI-TCGA Cosmic COSV5392, NCI-TCGA Cosmic COSV9967, Variant assessed as somatic; moderate impact.
- C138R (p.Cys138Arg), ExAC rs747533320, TOPMed rs747533320, gnomAD rs747533320, REVEL 0.43, ESM-1b 1.00
- C138S (p.Cys138Ser), TOPMed rs1162919810, gnomAD rs1162919810, REVEL 0.20, ESM-1b 0.97
- C138A (p.Cys138Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S139G (p.Ser139Gly), TOPMed rs946381757, REVEL 0.10, ESM-1b 0.00
- V140L (p.Val140Leu), gnomAD rs1944441105, REVEL 0.09, ESM-1b 0.28
- G141R (p.Gly141Arg), 1000Genomes rs149533049, ESP rs149533049, ExAC rs149533049, TOPMed rs149533049, REVEL 0.57, ESM-1b 1.00, Uncertain significance, not provided
- G141S (p.Gly141Ser), rs149533049, ClinGen CA291141, ClinVar RCV000125331, ClinVar RCV000329997, REVEL 0.43, ESM-1b 1.00, Benign/Likely benign, not specified; not provided; Glycogen storage disorder due to hepatic glycogen s
- I142F (p.Ile142Phe), TOPMed rs1944440958, gnomAD rs1944440958, REVEL 0.20, ESM-1b 1.00
- P143S (p.Pro143Ser), rs376712209, ClinGen CA6480201, ClinVar RCV001067910, ClinVar RCV005348302, REVEL 0.80, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency; Inborn ge
- Y144* (p.Tyr144Ter), ExAC rs753566404, CADD 34.00
- Y144H (p.Tyr144His), ExAC rs755209494, gnomAD rs755209494, REVEL 0.05, ESM-1b 0.00
- H145R (p.His145Arg), TOPMed rs1389217410, gnomAD rs1389217410, REVEL 0.20, ESM-1b 1.00
- D146A (p.Asp146Ala), Ensembl rs1591800646, REVEL 0.87, ESM-1b 1.00
- D146Y (p.Asp146Tyr), 1000Genomes rs187237403, ExAC rs187237403, gnomAD rs187237403, REVEL 0.74, ESM-1b 1.00
- R147* (p.Arg147Ter), TOPMed rs748996941, gnomAD rs748996941, CADD 37.00, Likely pathogenic
- R147P (p.Arg147Pro), ExAC rs760649869, TOPMed rs760649869, gnomAD rs760649869, REVEL 0.31, ESM-1b 1.00
- R147Q (p.Arg147Gln), rs760649869, NCI-TCGA Cosmic COSV5392, ExAC rs760649869, TOPMed rs760649869, REVEL 0.04, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- E148K (p.Glu148Lys), Ensembl rs1591800629, ESM-1b 1.00, AlphaMissense 0.95
- A149D (p.Ala149Asp), 1000Genomes rs573849661, gnomAD rs573849661, REVEL 0.56, ESM-1b 1.00
- N150S (p.Asn150Ser), ExAC rs773073036, TOPMed rs773073036, gnomAD rs773073036, REVEL 0.29, ESM-1b 0.60, Uncertain significance, Inborn genetic diseases
- D151N (p.Asp151Asn), ExAC rs767023189, TOPMed rs767023189, gnomAD rs767023189, REVEL 0.38, ESM-1b 1.00
- M152T (p.Met152Thr), 1000Genomes rs2136906068, REVEL 0.19, ESM-1b 1.00
- I154L (p.Ile154Leu), rs752480125, NCI-TCGA Cosmic COSV9967, Ensembl rs752480125, REVEL 0.09, ESM-1b 0.92, Variant assessed as somatic; moderate impact.
- I154M (p.Ile154Met), 1000Genomes rs200401082, ExAC rs200401082, TOPMed rs200401082, gnomAD rs200401082, REVEL 0.35, ESM-1b 1.00
- F155C (p.Phe155Cys), rs1364963978, ClinGen CA384137675, ClinVar RCV003628818, gnomAD rs1364963978, REVEL 0.64, ESM-1b 1.00, Uncertain significance, Glycogen storage disorder due to hepatic glycogen synthase deficiency
- F155L (p.Phe155Leu), TOPMed rs1308654670, ESM-1b 1.00, AlphaMissense 0.85
- S157C (p.Ser157Cys), ExAC rs774019135, TOPMed rs774019135, gnomAD rs774019135, REVEL 0.24, ESM-1b 0.00, Uncertain significance
- S157F (p.Ser157Phe), rs774019135, ClinGen CA6480192, ClinVar RCV001294991, ClinVar RCV005348408, REVEL 0.13, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Glycogen storage disorder due to hepatic glycogen synth
- S157Y (p.Ser157Tyr), ExAC rs774019135, TOPMed rs774019135, gnomAD rs774019135, REVEL 0.21, ESM-1b 0.00, Uncertain significance
Public GYS2 analysis runs
- GYS2 analysis run — GYS2 (1,088 variants) — completed 2026-10-09