Sugi Variant

Sugi Variant/PGAM2

PGAM2 — 190 ClinVar variants

All ClinVar germline PGAM2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 102 flagged for review →

8 Pathogenic · 3 Pathogenic/Likely pathogenic · 1 Likely pathogenic · 13 Conflicting · 5 Benign · 2 Benign/Likely benign · 54 Likely benign · 104 Uncertain significance

Full PGAM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 102

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 agree, ClinVar conflicts 3

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

Predictors lean, ClinVar uncertain 55

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 44

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

All PGAM2 variants

Pathogenic 8

  • p.Arg180Ter Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Cys55fs Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Gln111Ter Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ile54fs Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu71fs Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ser58Ter Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Trp25Ter Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Trp78Ter Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency

Pathogenic/Likely pathogenic 3

  • p.Gly178fs Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Trp78Ter Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Val7fs Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency

Likely pathogenic 1

Conflicting classifications of pathogenicity 13

  • c.415-3C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ala104Thr Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ala242= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Arg40Gln Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Cys153= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Glu236Ala Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu89Ala Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly97Asp Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ile160= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ile171Val Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Thr152Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr84= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr96= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency

Benign 5

  • p.Asp72= Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Gly108= Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ile114Ser Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.595+212T>C Single submitter
  • c.-50T>G Single submitter

Benign/Likely benign 2

  • c.596-3T>C Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Pro122= Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency

Likely benign 54

  • c.415-17G>A Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.-164C>T Multiple submitters
  • p.Pro147= Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr103= Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr212= Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.414+36T>C Single submitter
  • c.414+9C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.415-12T>C Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.415-12T>G Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.415-18C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.415-4C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.415-5C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.595+11C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.595+17G>A Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.596-17T>C Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.596-8C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.-32G>A Single submitter
  • c.-46A>G Single submitter
  • p.Ala104= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ala163= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ala177= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Arg21= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Arg240= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Arg5= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Asn168= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Asp127= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Asp27= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Glu110= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Gly12= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Gly192= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.His107= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.His11= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.His186= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ile114= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ile121= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu145= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu190= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu224= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu30= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu6= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Leu67= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Lys100= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Lys228= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Lys61= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Phe119= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Pro123= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Pro124= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Pro131= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr227= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr238= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr35= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr74= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Tyr92= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Thr15= No assertion criteria PGAM2-related disorder

Uncertain significance 104

  • p.Ala143Thr Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ala252Asp Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg10Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg162Gln Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg162Pro Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg240Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg5His Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg65His Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg83His Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg86Cys Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg90Trp Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Asn17Lys Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu128Lys Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly178Ser Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly24Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Ile171Leu Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Leu6Val Multiple submitters Inborn genetic diseases ⚠
  • p.Lys225Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Lys39Gln Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Met50Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Phe52Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Pro122Leu Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Pro123Leu Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Pro215His Multiple submitters Inborn genetic diseases ⚠
  • p.Thr103Met Multiple submitters Inborn genetic diseases ⚠
  • p.Thr212Met Multiple submitters Inborn genetic diseases ⚠
  • p.Thr238Met Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Thr57Met Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Thr84Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Trp167Cys Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Val172Gly Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Val7Met Multiple submitters glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Val82Leu Multiple submitters Inborn genetic diseases ⚠
  • c.414+6C>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.595+3G>T Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.596-7G>A Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • c.*35A>G Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ala105del Single submitter
  • p.Ala105Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala143Pro Single submitter Inborn genetic diseases ⚠
  • p.Ala161Val Single submitter Inborn genetic diseases ⚠
  • p.Ala204Val Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ala42Val Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ala48Val Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg10Gln Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg10Pro Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg117His Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg140His Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg141Gln Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg191Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg21His Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg240Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg240Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg5Cys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg62Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg65Cys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg83Cys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Arg86His Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Asn20Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn20Thr Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Asp120Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp120Gly Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Asp202Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln76Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln76Pro Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu110Asp Single submitter Inborn genetic diseases ⚠
  • p.Glu13Lys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu154Lys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu169Lys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu170del Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Glu36Lys Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Glu37Gly Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly12del Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Gly144Asp Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly148Arg Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly199Trp Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Gly213Val Single submitter Inborn genetic diseases ⚠
  • p.Gly94Asp Single submitter Inborn genetic diseases ⚠
  • p.His107Gln Single submitter Inborn genetic diseases ⚠
  • p.His186Tyr Single submitter Inborn genetic diseases ⚠
  • p.Ile136Val Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ile160Thr Single submitter Inborn genetic diseases ⚠
  • p.Ile193Thr Single submitter Inborn genetic diseases ⚠
  • p.Ile45Met Single submitter Inborn genetic diseases ⚠
  • p.Ile54Thr Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ile64Met Single submitter Inborn genetic diseases ⚠
  • p.Leu182Pro Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Leu210Val Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Lys106Asn Single submitter Inborn genetic diseases ⚠
  • p.Lys46Glu Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Lys61Arg Single submitter Inborn genetic diseases ⚠
  • p.Phe26Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro123Arg Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Pro125Leu Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Ser155Arg Single submitter Inborn genetic diseases ⚠
  • p.Ser201Ter Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Ser31Arg Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Thr74Met Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Thr84Asn Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Trp78Arg Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠
  • p.Tyr142= Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency
  • p.Val112Met Single submitter Inborn genetic diseases ⚠
  • p.Val59Ala Single submitter Inborn genetic diseases ⚠
  • p.Val82Met Single submitter glycogen storage disease due to phosphoglycerate mutase deficiency ⚠