PIGM — 156 ClinVar variants

All ClinVar germline PIGM variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 115 flagged for review →

1 Pathogenic · 1 Likely pathogenic · 3 Conflicting · 7 Benign · 3 Benign/Likely benign · 11 Likely benign · 130 Uncertain significance

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

⚑ Evidence disagreements 115

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 lean, ClinVar uncertain 98

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

Predictors split 17

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

All PIGM variants

Pathogenic 1

  • p.Asn134fs Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency

Likely pathogenic 1

  • p.Met1Thr Multiple submitters Inborn genetic diseases

Conflicting classifications of pathogenicity 3

  • p.Glu252= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Leu313= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Lys180Ter Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency

Benign 7

  • c.-137A>G Multiple submitters
  • p.Asn384Asp Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Leu194= Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Phe365Leu Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Pro273= Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Asp40= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Pro348Ser Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency

Benign/Likely benign 3

  • p.Arg60= Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Gly2= Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ser333= Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency

Likely benign 11

  • p.Ala146= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ala232= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ala72= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Gln381= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Leu43= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Leu98= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Phe175= Single submitter
  • p.Phe61= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ser289= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Thr63= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Tyr339= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency

Uncertain significance 130

  • p.Arg419fs Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Arg41Gln Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg46Lys Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Cys317Tyr Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Gln334Pro Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Glu217Gln Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Gly20Asp Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.His44Tyr Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Leu398Pro Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Leu80Val Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Lys180Glu Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Lys202Arg Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Met138Val Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Phe288Ser Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Phe34Leu Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Pro135Leu Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Pro348Ala Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Pro78Ser Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser152Phe Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Thr321Ala Multiple submitters ⚠
  • p.Thr77Ile Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Trp364Arg Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr173Cys Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr276Cys Multiple submitters hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ala124Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ala151Gly Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ala167= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ala167Val Single submitter ⚠
  • p.Ala176Pro Single submitter ⚠
  • p.Ala213Asp Single submitter ⚠
  • p.Ala226Ser Single submitter ⚠
  • p.Ala25Asp Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ala282Ser Single submitter ⚠
  • p.Ala58= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ala58Val Single submitter ⚠
  • p.Ala72Asp Single submitter ⚠
  • p.Arg122Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg122Leu Single submitter ⚠
  • p.Arg198Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg205Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg205Ser Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg41Pro Single submitter ⚠
  • p.Arg41Trp Single submitter ⚠
  • p.Arg66Cys Single submitter ⚠
  • p.Arg66Leu Single submitter ⚠
  • p.Arg71Lys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg75Gly Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Arg75His Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Asn13Ser Single submitter ⚠
  • p.Asn328Tyr Single submitter ⚠
  • p.Asn400Ser Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Asp423Glu Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Cys102Tyr Single submitter ⚠
  • p.Cys125Phe Single submitter ⚠
  • p.Cys128Arg Single submitter ⚠
  • p.Cys331Tyr Single submitter ⚠
  • p.Gln381fs Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Gln406Pro Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Glu217Lys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Glu248Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Gly20Ser Single submitter ⚠
  • p.Gly367Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Gly8Asp Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.His269Tyr Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.His44Arg Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.His6Asp Single submitter ⚠
  • p.Ile149= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ile149Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ile267Val Single submitter ⚠
  • p.Ile300Val Single submitter ⚠
  • p.Ile366Leu Single submitter ⚠
  • p.Ile50Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ile88Thr Single submitter ⚠
  • p.Leu14Ser Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Leu14Trp Single submitter ⚠
  • p.Leu153Arg Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Leu153Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Leu204Pro Single submitter ⚠
  • p.Leu229Gln Single submitter ⚠
  • p.Leu229Pro Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Leu32Pro Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Leu387fs Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Leu398Val Single submitter ⚠
  • p.Leu416Val Single submitter ⚠
  • p.Leu83His Single submitter ⚠
  • p.Leu98Ile Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Lys15Glu Single submitter ⚠
  • p.Lys383Met Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Met277Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Met347Lys Single submitter ⚠
  • p.Phe327Ser Single submitter ⚠
  • p.Phe365Val Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Phe38Leu Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Phe61Tyr Single submitter ⚠
  • p.Phe94= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Pro183Ser Single submitter ⚠
  • p.Pro273Leu Single submitter
  • p.Ser101Arg Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser141Cys Single submitter ⚠
  • p.Ser141Tyr Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser148= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Ser148Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser152Ala Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser203Asn Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser284Gly Single submitter ⚠
  • p.Ser3Phe Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Ser409Phe Single submitter ⚠
  • p.Thr237fs Single submitter
  • p.Thr257Ala Single submitter ⚠
  • p.Thr321Lys Single submitter PIGM-related disorder ⚠
  • p.Thr326Ile Single submitter ⚠
  • p.Thr73= Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
  • p.Thr85Ser Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr159Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr186Ter Single submitter
  • p.Tyr209Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr258Asn Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr279Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr309Cys Single submitter ⚠
  • p.Tyr310_Leu313delinsPhe Single submitter
  • p.Tyr35Cys Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Tyr376Cys Single submitter
  • p.Val184Ala Single submitter ⚠
  • p.Val227Ala Single submitter ⚠
  • p.Val314Ile Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Val330Gly Single submitter ⚠
  • p.Val377Gly Single submitter ⚠
  • p.Val54Leu Single submitter hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency ⚠
  • p.Val62Ile Single submitter ⚠
  • p.His320Arg No assertion criteria PIGM-related disorder ⚠