PYGM (P11217) variants and mutations
PYGM (also known as P11217) is a human protein-coding gene encoding a glycogen phosphorylase, muscle form protein. Muscle glycogen phosphorylase releases glucose-1-phosphate from glycogen during energy demand. Variants cause McArdle disease, which impairs exercise tolerance. This analysis covers 1,381 PYGM variants and mutations. Of these, 97% have computational variant effect predictions. Disease context includes glycogen storage disease V, Tip-toe gait, and hereditary disease. Example PYGM variants include M1I, M1L, and M1T.
Variant analysis overview
- Gene: PYGM
- Protein: P11217
- UniProt accession: P11217
- Organism: Homo sapiens
- Variants analyzed: 1381
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 1,167 unspecified-consequence records; 119 missense variants; 30 frameshift variants; 110 synonymous variants; 13 stop-gained variants; 4 in-frame deletions; 2 splice-region variants; 4 in-frame insertions; 1 protein altering variant; 4 substitution
- Prediction scores: 1,344 variants have prediction scores (97% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: glycogen storage disease V, Tip-toe gait, hereditary disease, disorder of glycogen metabolism, Acute rhabdomyolysis, macular dystrophy, retinal, retinal disorder, hereditary skeletal muscle disorder, rhabdomyolysis, Abnormality of metabolism/homeostasis, neurodegenerative disease, Disorder of carbohydrate metabolism.
Protein structure and variant hotspots
- Protein features: 3 binding sites; 10 post-translational modification sites.
- PTM context: 13 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, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Diseases linked to PYGM
Notable PYGM variants
Examples include M1I, M1L, M1T, M1V, R3G, R3Q, R3W, P4L. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs2496676087, ClinGen CA381113489, ClinVar RCV003498270, ESM-1b 1.00, AlphaMissense 0.38, Pathogenic, Glycogen storage disease, type V
- M1L (p.Met1Leu), rs267606993, ClinGen CA381113509, ClinVar RCV000668678, ClinGen CA270754, ESM-1b 1.00, AlphaMissense 0.14, Pathogenic/Likely pathogenic, Glycogen storage disease, type V
- M1T (p.Met1Thr), rs2058423391, ClinGen CA381113497, ClinVar RCV001244574, ESM-1b 1.00, AlphaMissense 0.47, Likely pathogenic, Glycogen storage disease, type V
- M1V (p.Met1Val), rs267606993, ClinGen CA252209, ClinVar RCV000002399, ClinVar RCV001579810, ESM-1b 1.00, AlphaMissense 0.11, Pathogenic, Glycogen storage disease, type V
- R3G (p.Arg3Gly), 1000Genomes rs199565370, ESP rs199565370, ExAC rs199565370, TOPMed rs199565370, REVEL 0.27, ESM-1b 0.00, Uncertain significance, not provided; Glycogen storage disease, type V
- R3Q (p.Arg3Gln), rs374812974, ClinGen CA6080395, ClinVar RCV000726186, ClinVar RCV001274029, REVEL 0.24, ESM-1b 0.00, Uncertain significance, not provided; Glycogen storage disease, type V
- R3W (p.Arg3Trp), rs199565370, ClinGen CA6080396, ClinVar RCV001105035, ClinVar RCV003346318, REVEL 0.53, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; Inborn genetic diseases
- P4L (p.Pro4Leu), ExAC rs752266996, TOPMed rs752266996, gnomAD rs752266996, REVEL 0.84, ESM-1b 1.00
- L5P (p.Leu5Pro), Ensembl rs2058423247, REVEL 0.68, ESM-1b 1.00, Benign, Tip-toe gait
- S6T (p.Ser6Thr), cosmic curated COSV51219, ExAC rs764749317, TOPMed rs764749317, gnomAD rs764749317, REVEL 0.21, ESM-1b 0.00
- Q8K (p.Gln8Lys), rs886048464, ClinGen CA10631142, ClinVar RCV000312915, Ensembl rs886048464, ESM-1b 1.00, AlphaMissense 0.10, Uncertain significance, Glycogen storage disease, type V
- Q8R (p.Gln8Arg), Ensembl rs2058423135, ESM-1b 1.00, AlphaMissense 0.10, Uncertain significance, Glycogen storage disease, type V
- K12R (p.Lys12Arg), ExAC rs772411515, gnomAD rs772411515, REVEL 0.51, ESM-1b 0.00
- I14T (p.Ile14Thr), TOPMed rs1388586019, gnomAD rs1388586019, REVEL 0.90, ESM-1b 1.00
- I14V (p.Ile14Val), TOPMed rs2058423017, REVEL 0.58, ESM-1b 0.06
- S15G (p.Ser15Gly), Ensembl rs1032877990, REVEL 0.70, ESM-1b 1.00
- V16A (p.Val16Ala), ExAC rs375188510, gnomAD rs375188510, REVEL 0.76, ESM-1b 0.74
- V16M (p.Val16Met), rs555856016, ClinGen CA223889435, ClinVar RCV002613288, 1000Genomes rs555856016, REVEL 0.70, ESM-1b 0.35, Uncertain significance, Glycogen storage disease, type V
- R17C (p.Arg17Cys), rs774650561, ExAC rs774650561, TOPMed rs774650561, gnomAD rs774650561, REVEL 0.81, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- R17G (p.Arg17Gly), ExAC rs774650561, TOPMed rs774650561, gnomAD rs774650561, ESM-1b 1.00, AlphaMissense 0.60
- R17H (p.Arg17His), rs148159796, ClinGen CA6080384, cosmic curated COSV10940, ClinVar RCV003063050, REVEL 0.81, ESM-1b 1.00, Uncertain significance, not provided; Inborn genetic diseases; Glycogen storage disease, type V
- L19P (p.Leu19Pro), gnomAD rs1196742852, REVEL 0.82, ESM-1b 0.00
- L19V (p.Leu19Val), 1000Genomes rs535560622, ExAC rs535560622, gnomAD rs535560622, REVEL 0.27, ESM-1b 0.00, Likely benign
- A20P (p.Ala20Pro), rs775674324, ExAC rs775674324, gnomAD rs775674324, ESM-1b 1.00, AlphaMissense 0.47, Variant assessed as somatic; moderate impact.
- A20T (p.Ala20Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G21S (p.Gly21Ser), rs145881639, ClinGen CA6080380, cosmic curated COSV51216, ClinVar RCV000726775, REVEL 0.58, ESM-1b 0.44, Uncertain significance, not provided; Glycogen storage disease, type V
- G21T (p.Gly21Thr), NCI-TCGA Cosmic COSV5121, Variant assessed as somatic; moderate impact.
- V22L (p.Val22Leu), ESP rs140731551, TOPMed rs140731551, gnomAD rs140731551, REVEL 0.32, ESM-1b 1.00, Uncertain significance
- V22M (p.Val22Met), rs140731551, ClinGen CA10606633, cosmic curated COSV51215, ClinVar RCV000396772, REVEL 0.35, ESM-1b 1.00, Uncertain significance, not provided; Glycogen storage disease, type V
- E23G (p.Glu23Gly), Ensembl rs760855386, ESM-1b 1.00, AlphaMissense 0.21
- E23D (p.Glu23Asp), TOPMed rs1403210693, ESM-1b 0.78, AlphaMissense 0.21
- V25M (p.Val25Met), ESP rs146845353, ExAC rs146845353, TOPMed rs146845353, gnomAD rs146845353, REVEL 0.67, ESM-1b 1.00
- T26I (p.Thr26Ile), ExAC rs777515712, gnomAD rs777515712, ESM-1b 0.00, AlphaMissense 0.19
- T26S (p.Thr26Ser), ExAC rs777515712, gnomAD rs777515712, REVEL 0.18, ESM-1b 0.00
- E27G (p.Glu27Gly), rs1305717617, ClinGen CA381112997, ClinVar RCV002664139, TOPMed rs1305717617, REVEL 0.30, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- E27K (p.Glu27Lys), gnomAD rs1434873172, REVEL 0.25, ESM-1b 1.00
- L28M (p.Leu28Met), TOPMed rs1592417170, gnomAD rs1592417170, REVEL 0.41, ESM-1b 1.00, Likely benign
- L28V (p.Leu28Val), TOPMed rs1592417170, gnomAD rs1592417170, REVEL 0.31, ESM-1b 1.00, Likely benign
- K30R (p.Lys30Arg), ExAC rs764779249, gnomAD rs764779249, ESM-1b 1.00, AlphaMissense 0.08
- N33K (p.Asn33Lys), rs2496675641, ClinGen CA381112886, ClinVar RCV004440639, ESM-1b 1.00, AlphaMissense 0.98, Uncertain significance, Inborn genetic diseases
- N33S (p.Asn33Ser), rs886048463, ClinGen CA10638975, ClinVar RCV000290610, TOPMed rs886048463, REVEL 0.46, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- R34Q (p.Arg34Gln), rs753484236, ClinGen CA6080371, ClinVar RCV003130368, ExAC rs753484236, REVEL 0.67, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- R34W (p.Arg34Trp), rs531748591, ClinGen CA6080372, ClinVar RCV001653163, ClinVar RCV001832839, REVEL 0.76, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; not provided
- H35Q (p.His35Gln), TOPMed rs2058422236, ESM-1b 1.00, AlphaMissense 0.98, Likely benign
- H35Y (p.His35Tyr), Ensembl rs2058422262, ESM-1b 1.00, AlphaMissense 0.81
- L36R (p.Leu36Arg), rs1394188143, ClinGen CA381112838, ClinVar RCV001205755, TOPMed rs1394188143, REVEL 0.92, ESM-1b 1.00, Conflicting interpretations, Glycogen storage disease, type V
- H37D (p.His37Asp), gnomAD rs2058422170, REVEL 0.66, ESM-1b 1.00
- H37R (p.His37Arg), rs1170598133, ClinGen CA381112828, ClinVar RCV001542478, gnomAD rs1170598133, REVEL 0.75, ESM-1b 1.00, Likely pathogenic, Glycogen storage disease, type V
- F38L (p.Phe38Leu), gnomAD rs1478945166, REVEL 0.78, ESM-1b 1.00
- T39A (p.Thr39Ala), ExAC rs762103405, gnomAD rs762103405, ESM-1b 1.00, AlphaMissense 0.68
- T39I (p.Thr39Ile), Ensembl rs897159798, REVEL 0.74, ESM-1b 1.00
- V41I (p.Val41Ile), rs764465584, ClinGen CA6080367, NCI-TCGA Cosmic COSV5122, cosmic curated COSV51220, REVEL 0.38, ESM-1b 0.90, Uncertain significance, Glycogen storage disease, type V
- R44C (p.Arg44Cys), rs763488434, ClinGen CA6080366, cosmic curated COSV99377, ClinVar RCV003603928, REVEL 0.79, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- R44H (p.Arg44His), rs567482511, ClinGen CA6080365, ClinVar RCV000280338, ClinVar RCV002519132, REVEL 0.74, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; not provided
- N45S (p.Asn45Ser), rs769985937, ClinGen CA6080364, ClinVar RCV002638099, ExAC rs769985937, REVEL 0.44, ESM-1b 0.65, Uncertain significance, Glycogen storage disease, type V
- A47T (p.Ala47Thr), gnomAD rs2058421813, REVEL 0.79, ESM-1b 1.00
- T48A (p.Thr48Ala), Ensembl rs1565538897, REVEL 0.55, ESM-1b 1.00
- P49Q (p.Pro49Gln), rs368649966, ClinGen CA6080359, ClinVar RCV003130372, ESP rs368649966, REVEL 0.30, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- R50* (p.Arg50Ter), rs116987552, ClinGen CA222884, cosmic curated COSV11340, ClinVar RCV000002388, CADD 34.00, Pathogenic
- R50G (p.Arg50Gly), 1000Genomes rs116987552, ESP rs116987552, ExAC rs116987552, TOPMed rs116987552, ESM-1b 1.00, AlphaMissense 0.81, Pathogenic
- R50Q (p.Arg50Gln), rs758175735, ClinGen CA6080358, cosmic curated COSV51223, ClinVar RCV001242840, REVEL 0.54, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Glycogen storage disease, type V
- D51G (p.Asp51Gly), rs397514631, ClinGen CA261238, ClinVar RCV000033140, TOPMed rs397514631, REVEL 0.86, ESM-1b 1.00, Likely pathogenic, Glycogen storage disease, type V
- Y52D (p.Tyr52Asp), Ensembl rs1420873872, ESM-1b 1.00, AlphaMissense 0.94
- F54V (p.Phe54Val), rs148839812, ClinGen CA6080357, ClinVar RCV000703766, ClinVar RCV000761777, REVEL 0.74, ESM-1b 1.00, Uncertain significance, not specified; Glycogen storage disease, type V; not provided
- F54Y (p.Phe54Tyr), rs375646075, ClinGen CA6080356, ClinVar RCV003129439, ClinVar RCV003135288, REVEL 0.59, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; not provided; Glycogen storage disease, type V
- A55T (p.Ala55Thr), gnomAD rs1331894446, REVEL 0.89, ESM-1b 1.00
- A55GfsX21, rs780193588, Pathogenic
- H58R (p.His58Arg), cosmic curated COSV51214, gnomAD rs1416006850, REVEL 0.42, ESM-1b 1.00
- T59I (p.Thr59Ile), ExAC rs754417088, gnomAD rs754417088, REVEL 0.69, ESM-1b 1.00
- T59N (p.Thr59Asn), ExAC rs754417088, gnomAD rs754417088, REVEL 0.71, ESM-1b 1.00
- V60M (p.Val60Met), rs765962705, ClinGen CA6080352, NCI-TCGA Cosmic COSV5122, cosmic curated COSV51225, REVEL 0.71, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; not provided
- R61C (p.Arg61Cys), rs1413461008, ClinGen CA381112285, cosmic curated COSV51222, ClinVar RCV001996818, REVEL 0.91, ESM-1b 1.00, Uncertain significance, not specified; Glycogen storage disease, type V
- R61G (p.Arg61Gly), TOPMed rs1413461008, gnomAD rs1413461008, REVEL 0.90, ESM-1b 1.00, Uncertain significance
- R61H (p.Arg61His), rs145514333, ClinGen CA238832, cosmic curated COSV51220, ClinVar RCV000173380, REVEL 0.80, ESM-1b 1.00, Conflicting interpretations, not specified; not provided; Glycogen storage disease, type V
- D62G (p.Asp62Gly), TOPMed rs2058421121, ESM-1b 1.00, AlphaMissense 0.98
- D62N (p.Asp62Asn), rs2058421138, ClinGen CA381112268, cosmic curated COSV99376, ClinVar RCV004440637, REVEL 0.65, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases
- D62Y (p.Asp62Tyr), TOPMed rs2058421138, ESM-1b 1.00, AlphaMissense 0.98, Uncertain significance
- H63L (p.His63Leu), Ensembl rs1592416979, ESM-1b 1.00, AlphaMissense 0.28
- H63Q (p.His63Gln), Ensembl rs2058421074, REVEL 0.68, ESM-1b 1.00
- L64F (p.Leu64Phe), rs2058421040, ClinGen CA381112214, ClinVar RCV004546315, gnomAD rs2058421040, REVEL 0.81, ESM-1b 1.00, Uncertain significance, not provided
- V65E (p.Val65Glu), gnomAD rs1208434944, REVEL 0.92, ESM-1b 1.00
- V65L (p.Val65Leu), rs149658961, 1000Genomes rs149658961, ESP rs149658961, ExAC rs149658961, REVEL 0.54, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- V65M (p.Val65Met), rs149658961, ClinGen CA6080349, cosmic curated COSV10632, ClinVar RCV001277996, REVEL 0.62, ESM-1b 0.82, Uncertain significance, Glycogen storage disease, type V
- G66A (p.Gly66Ala), NCI-TCGA Cosmic COSV5122, cosmic curated COSV51225, Variant assessed as somatic; moderate impact.
- G66V (p.Gly66Val), ExAC rs763289422, gnomAD rs763289422, REVEL 0.69, ESM-1b 1.00
- R67C (p.Arg67Cys), TOPMed rs957181304, gnomAD rs957181304, REVEL 0.83, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases; Glycogen storage disease, type V
- R67H (p.Arg67His), rs371357163, cosmic curated COSV51217, ESP rs371357163, TOPMed rs371357163, REVEL 0.78, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- W68* (p.Trp68Ter), rs1057516349, ClinGen CA16041507, ClinVar RCV000411559, TOPMed rs1057516349, Pathogenic
- R70C (p.Arg70Cys), rs765844107, ClinGen CA6080344, ClinVar RCV000489454, ClinVar RCV001272370, REVEL 0.92, ESM-1b 1.00, Uncertain significance, not provided; not specified; Glycogen storage disease, type V
- R70H (p.Arg70His), ExAC rs759631990, TOPMed rs759631990, gnomAD rs759631990, REVEL 0.78, ESM-1b 1.00, Uncertain significance, not provided
- R70G (p.Arg70Gly), ExAC rs765844107, TOPMed rs765844107, gnomAD rs765844107, REVEL 0.94, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- R70L (p.Arg70Leu), cosmic curated COSV10874, ExAC rs759631990, TOPMed rs759631990, gnomAD rs759631990, REVEL 0.83, ESM-1b 1.00, Uncertain significance
- R70P (p.Arg70Pro), ExAC rs759631990, TOPMed rs759631990, gnomAD rs759631990, REVEL 0.90, ESM-1b 1.00, Uncertain significance
- T71M (p.Thr71Met), ESP rs377713922, ExAC rs377713922, TOPMed rs377713922, gnomAD rs377713922, REVEL 0.86, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- T71R (p.Thr71Arg), rs377713922, ClinGen CA381112038, ClinVar RCV003087847, REVEL 0.92, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- Q73* (p.Gln73Ter), rs1057517361, ClinGen CA16041506, ClinVar RCV000409722, Ensembl rs1057517361, Likely pathogenic
- Q73H (p.Gln73His), TOPMed rs1182739938, gnomAD rs1182739938, REVEL 0.66, ESM-1b 1.00
- Q73P (p.Gln73Pro), ExAC rs760927188, gnomAD rs760927188, ESM-1b 1.00, AlphaMissense 0.99
- Q73R (p.Gln73Arg), ExAC rs760927188, gnomAD rs760927188, ESM-1b 1.00, AlphaMissense 0.76
- H74Q (p.His74Gln), rs2496674881, ClinGen CA381111955, ClinVar RCV003135175, ClinVar RCV005475363, ESM-1b 0.70, AlphaMissense 0.25, Uncertain significance, Inborn genetic diseases; Glycogen storage disease, type V
- H74R (p.His74Arg), TOPMed rs1450912823, gnomAD rs1450912823, REVEL 0.27, ESM-1b 1.00
- H74Y (p.His74Tyr), TOPMed rs1248467384, REVEL 0.26, ESM-1b 0.00
- Y75* (p.Tyr75Ter), rs773361937, ClinGen CA6080339, ClinVar RCV001382416, ExAC rs773361937, CADD 38.00, Pathogenic
- Y75C (p.Tyr75Cys), rs1449944847, ClinGen CA381111939, ClinVar RCV001508674, ClinVar RCV002567995, REVEL 0.86, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; not provided
- Y75F (p.Tyr75Phe), rs1449944847, ClinGen CA381111945, ClinVar RCV003130366, REVEL 0.67, ESM-1b 0.54, Uncertain significance, Glycogen storage disease, type V
- Y75H (p.Tyr75His), TOPMed rs1349100815, gnomAD rs1349100815, REVEL 0.65, ESM-1b 1.00
- Y76* (p.Tyr76Ter), rs2496674822, ClinGen CA381111913, ClinVar RCV003045214, CADD 23.90, Pathogenic
- Y76F (p.Tyr76Phe), TOPMed rs1466112694, gnomAD rs1466112694, REVEL 0.57, ESM-1b 1.00
- D79E (p.Asp79Glu), gnomAD rs1455517747, ESM-1b 1.00, AlphaMissense 0.94
- D79V (p.Asp79Val), Ensembl rs2058420265, ESM-1b 1.00, AlphaMissense 0.97
- D79Y (p.Asp79Tyr), TOPMed rs1025481959, gnomAD rs1025481959, REVEL 0.86, ESM-1b 1.00
- K81N (p.Lys81Asn), TOPMed rs2058420115, ESM-1b 1.00, AlphaMissense 1.00
- K81R (p.Lys81Arg), rs771895781, ClinGen CA6080338, cosmic curated COSV51214, ClinVar RCV003130370, REVEL 0.55, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- I83F (p.Ile83Phe), rs761616685, ClinGen CA6080320, ClinVar RCV003130371, ExAC rs761616685, REVEL 0.84, ESM-1b 1.00, Conflicting interpretations, Glycogen storage disease, type V
- Y84* (p.Tyr84Ter), rs1057517145, ClinGen CA16041505, ClinVar RCV000412392, TOPMed rs1057517145, CADD 36.00, Pathogenic
- Y84C (p.Tyr84Cys), ExAC rs774159335, gnomAD rs774159335, REVEL 0.74, ESM-1b 1.00
- Y84H (p.Tyr84His), gnomAD rs1344134587, REVEL 0.79, ESM-1b 1.00
- Y85* (p.Tyr85Ter), rs527236146, ClinGen CA345696, ClinVar RCV000128551, Ensembl rs527236146, CADD 37.00, Pathogenic
- Y85H (p.Tyr85His), rs373310140, ClinGen CA6080318, ClinVar RCV003135192, ESP rs373310140, REVEL 0.88, ESM-1b 1.00, Uncertain significance, not provided; Glycogen storage disease, type V
- Y91F (p.Tyr91Phe), TOPMed rs2058411913, ESM-1b 0.91, AlphaMissense 0.26
- Y91H (p.Tyr91His), rs2496671677, ClinGen CA381111442, ClinVar RCV003456777, ESM-1b 1.00, AlphaMissense 0.94, Uncertain significance, not provided
- Y91S (p.Tyr91Ser), TOPMed rs2058411913, REVEL 0.96, ESM-1b 1.00
- M92I (p.Met92Ile), Ensembl rs2135840908, REVEL 0.25, ESM-1b 1.00
- M92V (p.Met92Val), gnomAD rs1435533547, REVEL 0.59, ESM-1b 1.00
- G93V (p.Gly93Val), rs1085307918, ClinGen CA381111386, ClinVar RCV000489939, Ensembl rs1085307918, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic, not provided
- R94L (p.Arg94Leu), TOPMed rs2058411786, REVEL 0.90, ESM-1b 1.00
- R94W (p.Arg94Trp), rs370247862, ClinGen CA6080314, ClinVar RCV000557171, ClinVar RCV001540069, REVEL 0.91, ESM-1b 1.00, Pathogenic/Likely pathogenic, PYGM-related disorder; not provided; Glycogen storage disease, type V
- T95M (p.Thr95Met), rs375233791, ClinGen CA6080313, ClinVar RCV002012790, ESP rs375233791, REVEL 0.69, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- Q97* (p.Gln97Ter), TOPMed rs917916740
- Q97H (p.Gln97His), gnomAD rs1169625293, REVEL 0.61, ESM-1b 1.00
- T99A (p.Thr99Ala), Ensembl rs2058411654, ESM-1b 0.00, AlphaMissense 0.20
- M100I (p.Met100Ile), ExAC rs780840197, gnomAD rs780840197, REVEL 0.79, ESM-1b 0.00
- M100L (p.Met100Leu), TOPMed rs2058411628, ESM-1b 1.00, AlphaMissense 0.35, Uncertain significance, Glycogen storage disease, type V
- M100R (p.Met100Arg), ExAC rs528545908, TOPMed rs528545908, gnomAD rs528545908, REVEL 0.94, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- M100T (p.Met100Thr), ExAC rs528545908, TOPMed rs528545908, gnomAD rs528545908, REVEL 0.86, ESM-1b 1.00, Uncertain significance
- L103Q (p.Leu103Gln), TOPMed rs1427813602, REVEL 0.93, ESM-1b 1.00
- L103V (p.Leu103Val), rs2135840833, ClinGen CA381111163, ClinVar RCV001579117, Ensembl rs2135840833, REVEL 0.60, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- A104G (p.Ala104Gly), NCI-TCGA Cosmic COSV9937, cosmic curated COSV99377, SIFT 0.13, Variant assessed as somatic; moderate impact.
- A104S (p.Ala104Ser), Ensembl rs1032965056, REVEL 0.21, ESM-1b 0.00
- E106Q (p.Glu106Gln), gnomAD rs935327691, REVEL 0.33, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases; Glycogen storage disease, type V
- D110G (p.Asp110Gly), gnomAD rs1251356910, REVEL 0.83, ESM-1b 1.00
- E111* (p.Glu111Ter), rs779392056, ClinGen CA381110987, ClinVar RCV001814419, ExAC rs779392056, AlphaMissense 0.82, MetaLR 0.71, Likely pathogenic
- E111K (p.Glu111Lys), rs779392056, ClinGen CA6080308, NCI-TCGA Cosmic COSV9937, ClinVar RCV001767769, REVEL 0.73, ESM-1b 1.00, Uncertain significance, not provided
- A112D (p.Ala112Asp), TOPMed rs2058411300, REVEL 0.96, ESM-1b 1.00
- T113I (p.Thr113Ile), rs147571836, ClinGen CA6080306, ClinVar RCV001277995, ESP rs147571836, REVEL 0.28, ESM-1b 0.00, Uncertain significance, Glycogen storage disease, type V
- T113P (p.Thr113Pro), Ensembl rs1592415865, ESM-1b 1.00, AlphaMissense 0.89
- Q115E (p.Gln115Glu), gnomAD rs1310345038, REVEL 0.48, ESM-1b 1.00
- Q115H (p.Gln115His), rs2135840732, ClinGen CA381110884, ClinVar RCV002009686, Ensembl rs2135840732, REVEL 0.81, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- Q115L (p.Gln115Leu), gnomAD rs879158851, REVEL 0.84, ESM-1b 1.00
- Q115R (p.Gln115Arg), gnomAD rs879158851, REVEL 0.84, ESM-1b 1.00
- L116P (p.Leu116Pro), rs776680924, ClinGen CA6080276, ClinVar RCV000666659, UniProt VAR 014002, REVEL 0.95, ESM-1b 1.00, Pathogenic/Likely pathogenic, Glycogen storage disease, type V
- L116V (p.Leu116Val), rs759361512, ClinGen CA6080277, ClinVar RCV001277994, ExAC rs759361512, REVEL 0.69, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- M120I (p.Met120Ile), TOPMed rs1230252473, gnomAD rs1230252473, REVEL 0.32, ESM-1b 0.48, Uncertain significance, Inborn genetic diseases
- M120L (p.Met120Leu), rs886943655, ClinGen CA381109972, ClinVar RCV002837802, ESM-1b 1.00, AlphaMissense 0.12, Uncertain significance, Glycogen storage disease, type V
- M120T (p.Met120Thr), rs374898083, ClinGen CA6080274, ClinVar RCV002912827, ClinVar RCV006546150, REVEL 0.75, ESM-1b 1.00, Uncertain significance, not provided; Glycogen storage disease, type V
- M120V (p.Met120Val), TOPMed rs886943655, gnomAD rs886943655, REVEL 0.46, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V
- E121Q (p.Glu121Gln), Ensembl rs2058409959, REVEL 0.73, ESM-1b 1.00
- E122* (p.Glu122Ter), gnomAD rs1319212857, CADD 39.00
- E122G (p.Glu122Gly), gnomAD rs1320036556, REVEL 0.90, ESM-1b 1.00
- E124* (p.Glu124Ter), rs1555136459, ClinGen CA381109873, ClinVar RCV000668184, TOPMed rs1555136459, AlphaMissense 0.17, MetaLR 0.79, Pathogenic
- E124Q (p.Glu124Gln), TOPMed rs1555136459, REVEL 0.55, ESM-1b 0.75, Uncertain significance, Glycogen storage disease, type V
- E125K (p.Glu125Lys), Ensembl rs1592415687, REVEL 0.78, ESM-1b 1.00, Uncertain significance, not provided
- I126T (p.Ile126Thr), gnomAD rs1592415683, REVEL 0.56, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases
- E128G (p.Glu128Gly), TOPMed rs1383044080, gnomAD rs1383044080, REVEL 0.77, ESM-1b 1.00, Uncertain significance, not provided
- E128K (p.Glu128Lys), TOPMed rs1306098829, gnomAD rs1306098829, REVEL 0.67, ESM-1b 1.00
- A130S (p.Ala130Ser), gnomAD rs1385683915, REVEL 0.80, ESM-1b 1.00
- A130V (p.Ala130Val), rs200430286, ClinGen CA6080273, ClinVar RCV000994653, ClinVar RCV001103122, REVEL 0.85, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; not provided
- A130T (p.Ala130Thr), NCI-TCGA Cosmic COSV9937, cosmic curated COSV99377, Variant assessed as somatic; moderate impact.
- G131T (p.Gly131Thr), NCI-TCGA Cosmic COSV5121, cosmic curated COSV51216, MetaLR 0.94, MetaSVM 0.91, Variant assessed as somatic; moderate impact.
- G131A (p.Gly131Ala), Ensembl rs1358136040, ESM-1b 0.00, AlphaMissense 0.72
- G131R (p.Gly131Arg), rs2058409644, ClinGen CA381109721, ClinVar RCV001309764, Ensembl rs2058409644, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, Glycogen storage disease, type V
- G133C (p.Gly133Cys), TOPMed rs1085308021, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic
- G133S (p.Gly133Ser), rs1085308021, ClinGen CA381109682, ClinVar RCV000489796, TOPMed rs1085308021, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic, not provided
- N134K (p.Asn134Lys), ESP rs372262267, ExAC rs372262267, TOPMed rs372262267, gnomAD rs372262267, REVEL 0.81, ESM-1b 1.00, Likely benign
- G135A (p.Gly135Ala), gnomAD rs2058409484, REVEL 0.96, ESM-1b 1.00
- G135R (p.Gly135Arg), rs780246932, ClinGen CA6080270, NCI-TCGA Cosmic COSV9937, ClinVar RCV000761339, REVEL 0.99, ESM-1b 1.00, Conflicting interpretations, Glycogen storage disease, type V
- G135W (p.Gly135Trp), ExAC rs780246932, TOPMed rs780246932, gnomAD rs780246932, REVEL 0.99, ESM-1b 1.00, Pathogenic
- G136A (p.Gly136Ala), NCI-TCGA Cosmic COSV5122, cosmic curated COSV51221, REVEL 0.98, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- G136D (p.Gly136Asp), ExAC rs756547364, TOPMed rs756547364, gnomAD rs756547364, REVEL 0.99, ESM-1b 1.00, Likely pathogenic, Glycogen storage disease, type V
- G136S (p.Gly136Ser), rs1246112610, ClinGen CA381109629, ClinVar RCV003135183, ClinVar RCV005406636, REVEL 0.97, ESM-1b 1.00, Uncertain significance, Glycogen storage disease, type V; not specified; Inborn genetic diseases
Public PYGM analysis runs
- PYGM analysis run — PYGM (1,381 variants) — completed 2026-10-09