PYGM — 1508 ClinVar variants

All ClinVar germline PYGM variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 463 flagged for review →

93 Pathogenic · 63 Pathogenic/Likely pathogenic · 121 Likely pathogenic · 94 Conflicting · 33 Benign · 13 Benign/Likely benign · 621 Likely benign · 470 Uncertain significance

Full PYGM gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 463

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 41

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 297

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 297

Predictors split 123

The independent predictors disagree with each other — read with care.

All PYGM variants

Pathogenic 93

  • c.1239_1239+1delinsAT Multiple submitters glycogen storage disease V
  • c.1403+1G>A Multiple submitters glycogen storage disease V
  • p.Ala452fs Multiple submitters glycogen storage disease V
  • p.Ala55fs Multiple submitters glycogen storage disease V
  • p.Arg650Ter Multiple submitters glycogen storage disease V
  • p.Arg94Trp Multiple submitters glycogen storage disease V
  • p.Gln169Ter Multiple submitters glycogen storage disease V
  • p.Glu125fs Multiple submitters glycogen storage disease V
  • p.Glu27fs Multiple submitters PYGM-related disorder
  • p.Glu797fs Multiple submitters glycogen storage disease V
  • p.Gly136fs Multiple submitters glycogen storage disease V
  • p.Gly695Arg Multiple submitters disorder of glycogen metabolism
  • p.Leu493fs Multiple submitters glycogen storage disease V
  • p.Leu5fs Multiple submitters glycogen storage disease V
  • p.Lys609= Multiple submitters glycogen storage disease V
  • p.Met1Leu Multiple submitters glycogen storage disease V
  • p.Met1Val Multiple submitters glycogen storage disease V
  • p.Ser211fs Multiple submitters glycogen storage disease V
  • p.Thr692fs Multiple submitters glycogen storage disease V
  • p.Trp388fs Multiple submitters glycogen storage disease V
  • p.Tyr733Ter Multiple submitters glycogen storage disease V
  • p.Tyr75Ter Multiple submitters glycogen storage disease V
  • p.Tyr85Ter Multiple submitters PYGM-related disorder
  • c.1403+2T>C Single submitter glycogen storage disease V
  • c.1970-1G>A Single submitter glycogen storage disease V
  • c.772+1G>T Single submitter glycogen storage disease V
  • c.772+2_772+3del Single submitter glycogen storage disease V
  • c.773-2A>T Single submitter glycogen storage disease V
  • p.Ala155fs Single submitter glycogen storage disease V
  • p.Ala448fs Single submitter glycogen storage disease V
  • p.Ala696fs Single submitter glycogen storage disease V
  • p.Arg11fs Single submitter glycogen storage disease V
  • p.Arg185_Tyr186insTer Single submitter glycogen storage disease V
  • p.Arg387fs Single submitter glycogen storage disease V
  • p.Arg650fs Single submitter glycogen storage disease V
  • p.Asn259fs Single submitter glycogen storage disease V
  • p.Asn559fs Single submitter glycogen storage disease V
  • p.Asn728fs Single submitter glycogen storage disease V
  • p.Asp307fs Single submitter glycogen storage disease V
  • p.Asp43fs Single submitter glycogen storage disease V
  • p.Asp718fs Single submitter glycogen storage disease V
  • p.Gln337Ter Single submitter glycogen storage disease V
  • p.Gln666Ter Single submitter glycogen storage disease V
  • p.Gln730fs Single submitter glycogen storage disease V
  • p.Gln755fs Single submitter glycogen storage disease V
  • p.Glu124Ter Single submitter glycogen storage disease V
  • p.Glu358fs Single submitter glycogen storage disease V
  • p.Glu553Ter Single submitter glycogen storage disease V
  • p.Glu797_Trp798insTer Single submitter glycogen storage disease V
  • p.Gly133fs Single submitter glycogen storage disease V
  • p.Gly165fs Single submitter glycogen storage disease V
  • p.Gly174fs Single submitter glycogen storage disease V
  • p.Gly705fs Single submitter glycogen storage disease V
  • p.His37fs Single submitter glycogen storage disease V
  • p.His451_Ala457del Single submitter glycogen storage disease V
  • p.Ile459fs Single submitter glycogen storage disease V
  • p.Ile508fs Single submitter glycogen storage disease V
  • p.Ile621fs Single submitter glycogen storage disease V
  • p.Leu132fs Single submitter glycogen storage disease V
  • p.Leu19fs Single submitter glycogen storage disease V
  • p.Leu244fs Single submitter glycogen storage disease V
  • p.Leu268fs Single submitter glycogen storage disease V
  • p.Leu653fs Single submitter glycogen storage disease V
  • p.Leu791fs Single submitter glycogen storage disease V
  • p.Lys521Ter Single submitter glycogen storage disease V
  • p.Lys592Ter Single submitter glycogen storage disease V
  • p.Met1Ile Single submitter glycogen storage disease V
  • p.Met619fs Single submitter glycogen storage disease V
  • p.Phe38fs Single submitter glycogen storage disease V
  • p.Ser15fs Single submitter glycogen storage disease V
  • p.Thr372fs Single submitter glycogen storage disease V
  • p.Thr48fs Single submitter glycogen storage disease V
  • p.Thr817fs Single submitter glycogen storage disease V
  • p.Trp175fs Single submitter glycogen storage disease V
  • p.Trp190Ter Single submitter glycogen storage disease V
  • p.Trp216Ter Single submitter glycogen storage disease V
  • p.Trp245Ter Single submitter glycogen storage disease V
  • p.Trp366Ter Single submitter glycogen storage disease V
  • p.Tyr114fs Single submitter glycogen storage disease V
  • p.Tyr186Ter Single submitter glycogen storage disease V
  • p.Tyr227Ter Single submitter glycogen storage disease V
  • p.Tyr234fs Single submitter glycogen storage disease V
  • p.Tyr405Ter Single submitter glycogen storage disease V
  • p.Tyr53fs Single submitter glycogen storage disease V
  • p.Tyr588fs Single submitter glycogen storage disease V
  • p.Tyr76Ter Single submitter glycogen storage disease V
  • p.Val380fs Single submitter glycogen storage disease V
  • p.Val41fs Single submitter glycogen storage disease V
  • p.Val453fs Single submitter glycogen storage disease V
  • p.Val774fs Single submitter glycogen storage disease V
  • p.Glu541Ter No assertion criteria glycogen storage disease V
  • p.Leu396Pro No assertion criteria glycogen storage disease V
  • p.Lys575fs No assertion criteria glycogen storage disease V

Pathogenic/Likely pathogenic 63

  • c.1239+1G>A Multiple submitters PYGM-related disorder
  • c.1768+1G>A Multiple submitters PYGM-related disorder
  • c.1768+2T>G Multiple submitters glycogen storage disease V
  • c.1970-2A>T Multiple submitters glycogen storage disease V
  • c.2178-1G>A Multiple submitters glycogen storage disease V
  • c.2379+2_2379+3delinsAT Multiple submitters glycogen storage disease V
  • c.2380-1G>A Multiple submitters glycogen storage disease V
  • c.345+2T>A Multiple submitters glycogen storage disease V
  • c.425-26A>G Multiple submitters glycogen storage disease V
  • c.425-2A>G Multiple submitters glycogen storage disease V
  • c.661-601G>A Multiple submitters glycogen storage disease V
  • p.Ala704Val Multiple submitters glycogen storage disease V ⚠
  • p.Arg139Trp Multiple submitters glycogen storage disease V
  • p.Arg161_Tyr162insTer Multiple submitters glycogen storage disease V
  • p.Arg194fs Multiple submitters glycogen storage disease V
  • p.Arg270Ter Multiple submitters Acute rhabdomyolysis
  • p.Arg490fs Multiple submitters glycogen storage disease V
  • p.Arg490Gln Multiple submitters glycogen storage disease V
  • p.Arg50Ter Multiple submitters Skeletal muscle channelopathy
  • p.Arg570Gln Multiple submitters PYGM-related disorder
  • p.Arg576Ter Multiple submitters glycogen storage disease V
  • p.Arg771Gln Multiple submitters glycogen storage disease V ⚠
  • p.Asn168Ter Multiple submitters glycogen storage disease V
  • p.Asn454_Leu464del Multiple submitters glycogen storage disease V
  • p.Cys373Ter Multiple submitters glycogen storage disease V
  • p.Cys784Ter Multiple submitters PYGM-related disorder
  • p.Gln220fs Multiple submitters glycogen storage disease V
  • p.Gln220Ter Multiple submitters glycogen storage disease V
  • p.Glu349Lys Multiple submitters glycogen storage disease V
  • p.Glu383Lys Multiple submitters PYGM-related disorder
  • p.Glu573Ter Multiple submitters glycogen storage disease V
  • p.Glu655Lys Multiple submitters glycogen storage disease V
  • p.Gly455Arg Multiple submitters glycogen storage disease V
  • p.Gly686Arg Multiple submitters PYGM-related disorder
  • p.Ile308fs Multiple submitters glycogen storage disease V
  • p.Leu116Pro Multiple submitters glycogen storage disease V
  • p.Leu397Pro Multiple submitters glycogen storage disease V
  • p.Leu516fs Multiple submitters glycogen storage disease V
  • p.Leu587Pro Multiple submitters glycogen storage disease V
  • p.Lys10fs Multiple submitters glycogen storage disease V
  • p.Lys170del Multiple submitters glycogen storage disease V
  • p.Lys42fs Multiple submitters glycogen storage disease V
  • p.Lys543Thr Multiple submitters glycogen storage disease V
  • p.Lys754fs Multiple submitters PYGM-related disorder
  • p.Met351fs Multiple submitters glycogen storage disease V
  • p.Phe599fs Multiple submitters PYGM-related disorder
  • p.Phe710del Multiple submitters glycogen storage disease V
  • p.Phe759fs Multiple submitters glycogen storage disease V
  • p.Pro230fs Multiple submitters glycogen storage disease V
  • p.Pro489Arg Multiple submitters glycogen storage disease V
  • p.Ser430fs Multiple submitters glycogen storage disease V
  • p.Ser87fs Multiple submitters glycogen storage disease V
  • p.Trp183Ter Multiple submitters glycogen storage disease V
  • p.Trp492Ter Multiple submitters glycogen storage disease V
  • p.Trp68Ter Multiple submitters glycogen storage disease V
  • p.Trp798Arg Multiple submitters glycogen storage disease V
  • p.Tyr84fs Multiple submitters glycogen storage disease V
  • p.Tyr84Ter Multiple submitters glycogen storage disease V
  • p.Val456Met Multiple submitters glycogen storage disease V
  • p.Val503fs Multiple submitters glycogen storage disease V
  • p.Val716fs Multiple submitters glycogen storage disease V
  • p.Val788fs Multiple submitters glycogen storage disease V
  • p.Tyr574Ter No assertion criteria glycogen storage disease V

Likely pathogenic 121

  • c.1092+1G>A Multiple submitters glycogen storage disease V
  • c.1092+1G>C Multiple submitters glycogen storage disease V
  • c.1240-2A>G Multiple submitters PYGM-related disorder
  • c.1827+1G>C Multiple submitters glycogen storage disease V
  • c.1969+1G>A Multiple submitters glycogen storage disease V
  • c.1969+1G>C Multiple submitters glycogen storage disease V
  • c.1970-1G>C Multiple submitters glycogen storage disease V
  • c.2177_2177+3del Multiple submitters glycogen storage disease V
  • c.2177+1G>A Multiple submitters glycogen storage disease V
  • c.2177+1G>T Multiple submitters PYGM-related disorder
  • c.2313-1G>A Multiple submitters glycogen storage disease V
  • c.424+1G>T Multiple submitters glycogen storage disease V
  • c.528+2T>G Multiple submitters glycogen storage disease V
  • c.660+1G>A Multiple submitters glycogen storage disease V
  • c.772+2T>A Multiple submitters PYGM-related disorder
  • p.Asp284fs Multiple submitters glycogen storage disease V
  • p.Asp511fs Multiple submitters glycogen storage disease V
  • p.Asp51Gly Multiple submitters glycogen storage disease V
  • p.Asp694Glu Multiple submitters glycogen storage disease V
  • p.Gln73Ter Multiple submitters glycogen storage disease V
  • p.Leu137fs Multiple submitters PYGM-related disorder
  • p.Phe546fs Multiple submitters glycogen storage disease V
  • p.Ser450fs Multiple submitters PYGM-related disorder
  • p.Tyr85fs Multiple submitters glycogen storage disease V
  • c.1093-1G>A Single submitter glycogen storage disease V
  • c.1093-1G>C Single submitter glycogen storage disease V
  • c.1093-1G>T Single submitter glycogen storage disease V
  • c.1093-2A>T Single submitter glycogen storage disease V
  • c.1239+1G>T Single submitter glycogen storage disease V
  • c.1403+1dup Single submitter glycogen storage disease V
  • c.1404-1G>C Single submitter glycogen storage disease V
  • c.1518+1G>A Single submitter glycogen storage disease V
  • c.1519-1G>A Single submitter glycogen storage disease V
  • c.1519-2A>G Single submitter glycogen storage disease V
  • c.1519-3T>G Single submitter glycogen storage disease V
  • c.1620+1G>T Single submitter glycogen storage disease V
  • c.1769-1G>A Single submitter glycogen storage disease V
  • c.1828-1G>A Single submitter glycogen storage disease V
  • c.1828-1G>T Single submitter glycogen storage disease V
  • c.1828-2A>G Single submitter glycogen storage disease V
  • c.1970-2A>C Single submitter glycogen storage disease V
  • c.2313-2A>G Single submitter glycogen storage disease V
  • c.2379+1G>A Single submitter glycogen storage disease V
  • c.2380-1G>T Single submitter
  • c.2380-2A>G Single submitter glycogen storage disease V
  • c.243+1G>T Single submitter glycogen storage disease V
  • c.244-1G>A Single submitter glycogen storage disease V
  • c.424+1G>A Single submitter glycogen storage disease V
  • c.528+1G>A Single submitter glycogen storage disease V
  • c.528+1G>T Single submitter glycogen storage disease V
  • c.661-2A>C Single submitter glycogen storage disease V
  • c.772+1G>C Single submitter glycogen storage disease V
  • c.773-1G>C Single submitter glycogen storage disease V
  • c.855+1G>A Single submitter glycogen storage disease V
  • c.855+2T>C Single submitter glycogen storage disease V
  • c.856-2A>C Single submitter glycogen storage disease V
  • c.999+1G>A Single submitter glycogen storage disease V
  • p.Ala365Glu Single submitter glycogen storage disease V
  • p.Ala384Val Single submitter glycogen storage disease V
  • p.Ala660Asp Single submitter glycogen storage disease V
  • p.Arg139Gly Single submitter glycogen storage disease V
  • p.Arg161His Single submitter glycogen storage disease V
  • p.Arg17fs Single submitter glycogen storage disease V
  • p.Arg490Pro Single submitter glycogen storage disease V
  • p.Arg67fs Single submitter glycogen storage disease V
  • p.Asn33fs Single submitter glycogen storage disease V
  • p.Asn45fs Single submitter glycogen storage disease V
  • p.Asp228fs Single submitter glycogen storage disease V
  • p.Asp422fs Single submitter glycogen storage disease V
  • p.Cys496_Asn497delinsTer Single submitter glycogen storage disease V
  • p.Cys581fs Single submitter glycogen storage disease V
  • p.Glu111Ter Single submitter Abnormality of metabolism/homeostasis
  • p.Glu23fs Single submitter glycogen storage disease V
  • p.Glu288Ter Single submitter glycogen storage disease V
  • p.Glu297Ter Single submitter glycogen storage disease V
  • p.Glu349fs Single submitter glycogen storage disease V
  • p.Glu462fs Single submitter glycogen storage disease V
  • p.Glu786fs Single submitter glycogen storage disease V
  • p.Glu786Ter Single submitter glycogen storage disease V
  • p.Gly133Ser Single submitter
  • p.Gly136Asp Single submitter glycogen storage disease V
  • p.Gly157Val Single submitter glycogen storage disease V
  • p.Gly174Asp Single submitter glycogen storage disease V
  • p.Gly205Cys Single submitter glycogen storage disease V
  • p.Gly686Glu Single submitter glycogen storage disease V
  • p.Gly695Trp Single submitter glycogen storage disease V
  • p.Gly93Val Single submitter
  • p.His451fs Single submitter glycogen storage disease V
  • p.Ile276fs Single submitter glycogen storage disease V
  • p.Ile336fs Single submitter glycogen storage disease V
  • p.Leu280fs Single submitter glycogen storage disease V
  • p.Leu36Pro Single submitter glycogen storage disease V
  • p.Leu40fs Single submitter glycogen storage disease V
  • p.Leu426fs Single submitter glycogen storage disease V
  • p.Leu579del Single submitter glycogen storage disease V
  • p.Lys483fs Single submitter glycogen storage disease V
  • p.Lys575Glu Single submitter glycogen storage disease V
  • p.Lys681fs Single submitter glycogen storage disease V
  • p.Met1_Pro4del Single submitter glycogen storage disease V
  • p.Met1fs Single submitter glycogen storage disease V
  • p.Met1Thr Single submitter glycogen storage disease V
  • p.Phe709fs Single submitter glycogen storage disease V
  • p.Ser809fs Single submitter glycogen storage disease V
  • p.Trp798Gly Single submitter glycogen storage disease V
  • p.Trp798Ter Single submitter glycogen storage disease V
  • p.Tyr158fs Single submitter glycogen storage disease V
  • p.Tyr281Ter Single submitter PYGM-related disorder
  • p.Tyr53del Single submitter glycogen storage disease V
  • p.Tyr727Ter Single submitter glycogen storage disease V
  • p.Val16fs Single submitter glycogen storage disease V
  • p.Val231fs Single submitter glycogen storage disease V
  • p.Val651Leu Single submitter glycogen storage disease V
  • c.1969+1G>T No assertion criteria glycogen storage disease V
  • p.Ala149fs No assertion criteria glycogen storage disease V
  • p.Asn561fs No assertion criteria glycogen storage disease V
  • p.Glu744fs No assertion criteria glycogen storage disease V
  • p.Gly713fs No assertion criteria glycogen storage disease V
  • p.His37Arg No assertion criteria glycogen storage disease V
  • p.His74fs No assertion criteria glycogen storage disease V
  • p.Leu88fs No assertion criteria glycogen storage disease V
  • p.Ter843Leu No assertion criteria glycogen storage disease V

Conflicting classifications of pathogenicity 94

Benign 33

Benign/Likely benign 13

  • c.1240-16G>A Multiple submitters glycogen storage disease V
  • c.1519-12G>A Multiple submitters glycogen storage disease V
  • c.1621-19del Multiple submitters glycogen storage disease V
  • c.1970-6C>T Multiple submitters Tip-toe gait
  • c.424+17G>A Multiple submitters glycogen storage disease V
  • c.661-5C>G Multiple submitters glycogen storage disease V
  • p.Ala193Ser Multiple submitters glycogen storage disease V ⚠
  • p.Ala670Val Multiple submitters glycogen storage disease V
  • p.Asn794= Multiple submitters glycogen storage disease V
  • p.Glu703= Multiple submitters glycogen storage disease V
  • p.Gly509= Multiple submitters glycogen storage disease V
  • p.His202= Multiple submitters glycogen storage disease V
  • p.Tyr405= Multiple submitters glycogen storage disease V

Likely benign 621

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 470

Showing the top 300 by review status; the full set is in the sitemap.