GPI — 240 ClinVar variants

All ClinVar germline GPI variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 124 flagged for review →

14 Pathogenic · 6 Pathogenic/Likely pathogenic · 13 Likely pathogenic · 12 Conflicting · 13 Benign · 6 Benign/Likely benign · 60 Likely benign · 116 Uncertain significance

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

⚑ Evidence disagreements 124

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 8

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

Predictors agree, ClinVar conflicts 5

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

Predictors lean, ClinVar uncertain 68

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

Predictors split 43

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

All GPI variants

Pathogenic 14

  • p.Arg472Cys Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Glu82fs Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ala337Val Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg273His Single submitter
  • p.Arg472His Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Asp539Asn Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Glu382Ter Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Gly87Cys Single submitter
  • p.Trp380Ter Single submitter
  • p.Val101Met Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.His20Pro No assertion criteria hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Leu339Pro No assertion criteria hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Thr375Arg No assertion criteria hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Thr5Ile No assertion criteria hemolytic anemia due to glucophosphate isomerase deficiency ⚠

Pathogenic/Likely pathogenic 6

  • p.Ala337Thr Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg347Cys Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Arg347His Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg446Ter Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Arg96Ter Multiple submitters GPI-related disorders
  • p.Gln343Arg Multiple submitters GPI-related disorders

Likely pathogenic 13

  • c.1269+1G>A Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • c.1475-2A>G Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • c.283-2A>G Single submitter hereditary spherocytosis
  • c.804+1_804+2del Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • c.866-1G>A Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Gln388fs Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Gly271fs Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ile280Val Single submitter ⚠
  • p.Ser278Leu Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Tyr17fs Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Val318fs Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Val500fs Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Gln28Ter No assertion criteria GPI-related disorder

Conflicting classifications of pathogenicity 12

  • c.1270-9G>A Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • c.214-12G>A Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ala232Val Single submitter Inborn genetic diseases ⚠
  • p.Ala533Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg106Gln Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg308His Single submitter Inborn genetic diseases ⚠
  • p.Ile525Thr Single submitter Inborn genetic diseases ⚠
  • p.Met303Leu Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Pro409= Single submitter
  • p.Pro456Ala Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr224Met Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Tyr341Cys Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠

Benign 13

Benign/Likely benign 6

  • c.486+7A>G Multiple submitters
  • c.751-5dup Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ala452= Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Asn329= Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ile208Thr Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Pro201= Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency

Likely benign 60

Uncertain significance 116

  • c.909+5G>A Multiple submitters
  • p.Ala350Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Ala540Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Arg135His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg370His Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg553Cys Multiple submitters Inborn genetic diseases
  • p.Arg556Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Arg6Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg83Trp Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Asp31His Multiple submitters Inborn genetic diseases ⚠
  • p.His191Arg Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ile477Met Multiple submitters Inborn genetic diseases ⚠
  • p.Lys466Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Lys550Glu Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ser441Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Ser532Gly Multiple submitters Inborn genetic diseases ⚠
  • p.Thr214Ala Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr309Met Multiple submitters hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr442Met Multiple submitters Inborn genetic diseases ⚠
  • p.Val181Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Val500Ile Multiple submitters Inborn genetic diseases ⚠
  • c.1542-7_1542-6delinsCC Single submitter
  • c.634-3C>T Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • c.866-8T>C Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • c.-9A>G Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ala232Glu Single submitter ⚠
  • p.Ala240= Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Ala240Val Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ala316Thr Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ala350Val Single submitter Inborn genetic diseases ⚠
  • p.Arg135Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg180His Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg273Cys Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg273Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg370Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg438Thr Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg446Gln Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg81Gln Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg81Trp Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg96Gln Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Arg96Gly Single submitter ⚠
  • p.Asn154Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn186Ser Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Asn547Ser Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Asp117Tyr Single submitter ⚠
  • p.Asp140Asn Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Asp235Glu Single submitter GPI-related disorder ⚠
  • p.Asp291Val Single submitter Inborn genetic diseases ⚠
  • p.Asp458Asn Single submitter Inborn genetic diseases ⚠
  • p.Cys333Tyr Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gln261Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln295His Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gln413Arg Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gln552His Single submitter Inborn genetic diseases ⚠
  • p.Glu227Val Single submitter Inborn genetic diseases ⚠
  • p.Glu294Lys Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Glu444Lys Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Glu495Gly Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Glu516Lys Single submitter ⚠
  • p.Glu82Gln Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gly139Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly159Ser Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gly361Arg Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gly453Val Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gly49Ala Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Gly95Cys Single submitter Inborn genetic diseases ⚠
  • p.His301Tyr Single submitter Inborn genetic diseases ⚠
  • p.His389Arg Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.His421Gln Single submitter Inborn genetic diseases ⚠
  • p.His538Gln Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ile187Thr Single submitter ⚠
  • p.Ile208Val Single submitter Inborn genetic diseases ⚠
  • p.Ile219Met Single submitter Inborn genetic diseases ⚠
  • p.Ile284Thr Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ile378Val Single submitter ⚠
  • p.Ile90Leu Single submitter ⚠
  • p.Leu319Val Single submitter Inborn genetic diseases ⚠
  • p.Leu4Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu529Val Single submitter ⚠
  • p.Leu545fs Single submitter hemolytic anemia due to glucophosphate isomerase deficiency
  • p.Lys12Gln Single submitter Inborn genetic diseases ⚠
  • p.Lys226Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys400Arg Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Lys523Thr Single submitter Inborn genetic diseases ⚠
  • p.Met338Val Single submitter Inborn genetic diseases ⚠
  • p.Met493Ile Single submitter Inborn genetic diseases
  • p.Phe213Ile Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Phe40Leu Single submitter ⚠
  • p.Pro164Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro527Ala Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Pro527Thr Single submitter Inborn genetic diseases ⚠
  • p.Ser131Thr Single submitter Inborn genetic diseases ⚠
  • p.Ser138Asn Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ser176Leu Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ser283Thr Single submitter ⚠
  • p.Ser298Ala Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ser41Gly Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Ser532Thr Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr109Ile Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr190Ile Single submitter ⚠
  • p.Thr195Ile Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr215Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr365Ile Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Thr474Ala Single submitter ⚠
  • p.Thr483Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr536Ile Single submitter intellectual disability, autosomal recessive 42 ⚠
  • p.Thr61Met Single submitter Inborn genetic diseases ⚠
  • p.Trp269Arg Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Trp513Arg Single submitter Inborn genetic diseases ⚠
  • p.Tyr174Cys Single submitter Inborn genetic diseases ⚠
  • p.Val152Ile Single submitter ⚠
  • p.Val253Leu Single submitter Inborn genetic diseases ⚠
  • p.Val467Ile Single submitter Inborn genetic diseases ⚠
  • p.Val478Ala Single submitter ⚠
  • p.Val64Met Single submitter hemolytic anemia due to glucophosphate isomerase deficiency ⚠
  • p.Val77Met Single submitter Inborn genetic diseases ⚠