HAP1 — 140 ClinVar variants
All ClinVar germline HAP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 107 flagged for review →
11 Benign · 20 Likely benign · 109 Uncertain significance
Full HAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 107
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 97
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- HAP1 p.Arg106Pro Uncertain significance Multiple submitters
- HAP1 p.Ala117Val Uncertain significance Single submitter
- HAP1 p.Ala11Thr Uncertain significance Single submitter
- HAP1 p.Ala126Glu Uncertain significance Single submitter
- HAP1 p.Ala126Val Uncertain significance Single submitter
- HAP1 p.Ala149Val Uncertain significance Single submitter
- HAP1 p.Ala230Val Uncertain significance Single submitter
- HAP1 p.Ala275Thr Uncertain significance Single submitter
- HAP1 p.Ala284Thr Uncertain significance Single submitter
- HAP1 p.Ala316Gly Uncertain significance Single submitter
- HAP1 p.Ala359Thr Uncertain significance Single submitter
- HAP1 p.Ala385Ser Uncertain significance Single submitter
- HAP1 p.Ala516Ser Uncertain significance Single submitter
- HAP1 p.Ala54Gly Uncertain significance Single submitter
- HAP1 p.Ala559Val Uncertain significance Single submitter
- HAP1 p.Ala74Val Uncertain significance Single submitter
- HAP1 p.Arg138Gln Uncertain significance Single submitter
- HAP1 p.Arg147His Uncertain significance Single submitter
- HAP1 p.Arg379Trp Uncertain significance Single submitter
- HAP1 p.Arg397Cys Uncertain significance Single submitter
- HAP1 p.Arg399Trp Uncertain significance Single submitter
- HAP1 p.Arg478Gln Uncertain significance Single submitter
- HAP1 p.Arg482Trp Uncertain significance Single submitter
- HAP1 p.Arg498Gln Uncertain significance Single submitter
- HAP1 p.Arg498Trp Uncertain significance Single submitter
- HAP1 p.Arg589Gln Uncertain significance Single submitter
- HAP1 p.Arg589Leu Uncertain significance Single submitter
- HAP1 p.Arg589Trp Uncertain significance Single submitter
- HAP1 p.Arg5Gly Uncertain significance Single submitter
- HAP1 p.Arg5Met Uncertain significance Single submitter
- HAP1 p.Arg65Ser Uncertain significance Single submitter
- HAP1 p.Arg8Gly Uncertain significance Single submitter
- HAP1 p.Asn218Ser Uncertain significance Single submitter
- HAP1 p.Asn554Thr Uncertain significance Single submitter
- HAP1 p.Asp265Asn Uncertain significance Single submitter
- HAP1 p.Asp92Val Uncertain significance Single submitter
- HAP1 p.Cys10Phe Uncertain significance Single submitter
- HAP1 p.Cys294Ser Uncertain significance Single submitter
- HAP1 p.Cys9Ser Uncertain significance Single submitter
- HAP1 p.Cys9Tyr Uncertain significance Single submitter
- HAP1 p.Gln308Pro Uncertain significance Single submitter
- HAP1 p.Gln380Arg Uncertain significance Single submitter
- HAP1 p.Gln390Glu Uncertain significance Single submitter
- HAP1 p.Gln419Arg Uncertain significance Single submitter
- HAP1 p.Gln421Arg Uncertain significance Single submitter
- HAP1 p.Glu237Lys Uncertain significance Single submitter
- HAP1 p.Glu283Ala Uncertain significance Single submitter
- HAP1 p.Glu303Lys Uncertain significance Single submitter
- HAP1 p.Glu334Lys Uncertain significance Single submitter
- HAP1 p.Glu344Asp Uncertain significance Single submitter
- HAP1 p.Glu351Gln Uncertain significance Single submitter
- HAP1 p.Glu351Lys Uncertain significance Single submitter
- HAP1 p.Glu455Lys Uncertain significance Single submitter
- HAP1 p.Glu488Lys Uncertain significance Single submitter
- HAP1 p.Glu506Lys Uncertain significance Single submitter
- HAP1 p.Glu538Lys Uncertain significance Single submitter
- HAP1 p.Gly127Asp Uncertain significance Single submitter
- HAP1 p.Gly499Arg Uncertain significance Single submitter
- HAP1 p.Gly564Ser Uncertain significance Single submitter
- HAP1 p.Gly7Asp Uncertain significance Single submitter
- HAP1 p.His309Tyr Uncertain significance Single submitter
- HAP1 p.Leu185His Uncertain significance Single submitter
- HAP1 p.Leu214Pro Uncertain significance Single submitter
- HAP1 p.Leu288Val Uncertain significance Single submitter
- HAP1 p.Leu338Phe Uncertain significance Single submitter
- HAP1 p.Leu570Val Uncertain significance Single submitter
- HAP1 p.Lys167Arg Uncertain significance Single submitter
- HAP1 p.Lys594Thr Uncertain significance Single submitter
- HAP1 p.Met446Arg Uncertain significance Single submitter
- HAP1 p.Met497Ile Uncertain significance Single submitter
- HAP1 p.Met572Val Uncertain significance Single submitter
- HAP1 p.Met96Ile Uncertain significance Single submitter
- HAP1 p.Phe60Leu Uncertain significance Single submitter
- HAP1 p.Pro163Leu Uncertain significance Single submitter
- HAP1 p.Pro17His Uncertain significance Single submitter
- HAP1 p.Pro37Leu Uncertain significance Single submitter
- HAP1 p.Pro37Ser Uncertain significance Single submitter
- HAP1 p.Pro3Leu Uncertain significance Single submitter
- HAP1 p.Pro521Leu Uncertain significance Single submitter
- HAP1 p.Pro567Leu Uncertain significance Single submitter
- HAP1 p.Pro97Ala Uncertain significance Single submitter
- HAP1 p.Ser115Phe Uncertain significance Single submitter
- HAP1 p.Ser301Leu Uncertain significance Single submitter
- HAP1 p.Ser414Leu Uncertain significance Single submitter
- HAP1 p.Ser414Trp Uncertain significance Single submitter
- HAP1 p.Ser475Asn Uncertain significance Single submitter
- HAP1 p.Ser52Cys Uncertain significance Single submitter
- HAP1 p.Ser617Leu Uncertain significance Single submitter
- HAP1 p.Thr503Met Uncertain significance Single submitter
- HAP1 p.Thr55Ile Uncertain significance Single submitter
- HAP1 p.Trp593Cys Uncertain significance Single submitter
- HAP1 p.Tyr179Cys Uncertain significance Single submitter
- HAP1 p.Tyr179His Uncertain significance Single submitter
- HAP1 p.Val166Leu Uncertain significance Single submitter
- HAP1 p.Val509Leu Uncertain significance Single submitter
- HAP1 p.Val509Met Uncertain significance Single submitter
- HAP1 p.Val543Met Uncertain significance Single submitter
Predictors split 10
The independent predictors disagree with each other — read with care.
- HAP1 p.Val369Ala Benign Multiple submitters
- HAP1 p.Arg249Pro Uncertain significance Single submitter
- HAP1 p.Gln330Pro Uncertain significance Single submitter
- HAP1 p.Glu269Gly Uncertain significance Single submitter
- HAP1 p.Glu270Gly Uncertain significance Single submitter
- HAP1 p.Leu214Met Uncertain significance Single submitter
- HAP1 p.Leu341Pro Uncertain significance Single submitter
- HAP1 p.Leu370Pro Uncertain significance Single submitter
- HAP1 p.Tyr135Asn Uncertain significance Single submitter
-
HAP1 p.Leu408Phe
Benign
No assertion criteria
HAP1-related disorder
All HAP1 variants
Benign 11
- p.Cys25Tyr Multiple submitters
- p.Gly604Arg Multiple submitters
- p.Ile496Val Multiple submitters
- p.Leu348= Multiple submitters
- p.Ser616Ter Multiple submitters
- p.Thr441Met Multiple submitters
- p.Val369Ala Multiple submitters ⚠
- p.Ala505Val No assertion criteria HAP1-related disorder
- p.Leu408Phe No assertion criteria HAP1-related disorder ⚠
- p.Pro521= No assertion criteria HAP1-related disorder
- p.Trp104Ter No assertion criteria HAP1-related disorder
Likely benign 20
- p.Thr66Ala Multiple submitters
- p.Arg209Cys Single submitter
- p.Arg399Gln Single submitter
- p.Arg482Gln Single submitter
- p.Arg8Trp Single submitter
- p.Cys9Gly Single submitter
- p.Thr427Ala Single submitter
- p.Tyr194His Single submitter
- p.Val555Met Single submitter
- c.1201-4C>T No assertion criteria HAP1-related disorder
- c.1201-7C>T No assertion criteria HAP1-related disorder
- c.470-7C>G No assertion criteria HAP1-related disorder
- c.550-3dup No assertion criteria HAP1-related disorder
- p.Ala21= No assertion criteria HAP1-related disorder
- p.Arg116Trp No assertion criteria HAP1-related disorder
- p.Asp339Asn No assertion criteria HAP1-related disorder
- p.Pro187His No assertion criteria HAP1-related disorder
- p.Thr434= No assertion criteria HAP1-related disorder
- p.Thr441= No assertion criteria HAP1-related disorder
- p.Thr503= No assertion criteria HAP1-related disorder
Uncertain significance 109
- p.Arg106Pro Multiple submitters ⚠
- p.Ala117Val Single submitter ⚠
- p.Ala11Thr Single submitter ⚠
- p.Ala126Glu Single submitter ⚠
- p.Ala126Val Single submitter ⚠
- p.Ala149Val Single submitter ⚠
- p.Ala230Val Single submitter ⚠
- p.Ala275Thr Single submitter ⚠
- p.Ala284Thr Single submitter ⚠
- p.Ala316Gly Single submitter ⚠
- p.Ala359Thr Single submitter ⚠
- p.Ala385Ser Single submitter ⚠
- p.Ala516Ser Single submitter ⚠
- p.Ala54Gly Single submitter ⚠
- p.Ala559Val Single submitter ⚠
- p.Ala605fs Single submitter HAP1-related disorder
- p.Ala74Val Single submitter ⚠
- p.Arg138Gln Single submitter ⚠
- p.Arg147His Single submitter ⚠
- p.Arg249Pro Single submitter ⚠
- p.Arg379Trp Single submitter ⚠
- p.Arg397Cys Single submitter ⚠
- p.Arg399Trp Single submitter ⚠
- p.Arg478Gln Single submitter ⚠
- p.Arg482Trp Single submitter ⚠
- p.Arg498Gln Single submitter ⚠
- p.Arg498Trp Single submitter ⚠
- p.Arg589Gln Single submitter ⚠
- p.Arg589Leu Single submitter ⚠
- p.Arg589Trp Single submitter ⚠
- p.Arg5Gly Single submitter ⚠
- p.Arg5Met Single submitter ⚠
- p.Arg65Ser Single submitter ⚠
- p.Arg8Gly Single submitter ⚠
- p.Asn218Ser Single submitter ⚠
- p.Asn554Thr Single submitter ⚠
- p.Asp265Asn Single submitter ⚠
- p.Asp92Val Single submitter ⚠
- p.Cys10Phe Single submitter ⚠
- p.Cys294Ser Single submitter ⚠
- p.Cys9Ser Single submitter ⚠
- p.Cys9Tyr Single submitter ⚠
- p.Gln308Pro Single submitter ⚠
- p.Gln330Pro Single submitter ⚠
- p.Gln380Arg Single submitter ⚠
- p.Gln390Glu Single submitter ⚠
- p.Gln419Arg Single submitter ⚠
- p.Gln421Arg Single submitter ⚠
- p.Glu229Lys Single submitter
- p.Glu237Lys Single submitter ⚠
- p.Glu269Gly Single submitter ⚠
- p.Glu270Gly Single submitter ⚠
- p.Glu283Ala Single submitter ⚠
- p.Glu303Lys Single submitter ⚠
- p.Glu334Lys Single submitter ⚠
- p.Glu344Asp Single submitter ⚠
- p.Glu351Gln Single submitter ⚠
- p.Glu351Lys Single submitter ⚠
- p.Glu455Lys Single submitter ⚠
- p.Glu488Lys Single submitter ⚠
- p.Glu506Lys Single submitter ⚠
- p.Glu538Lys Single submitter ⚠
- p.Gly127Asp Single submitter ⚠
- p.Gly499Arg Single submitter ⚠
- p.Gly564Ser Single submitter ⚠
- p.Gly7Asp Single submitter ⚠
- p.His309Tyr Single submitter ⚠
- p.Leu185His Single submitter ⚠
- p.Leu214Met Single submitter ⚠
- p.Leu214Pro Single submitter ⚠
- p.Leu288Val Single submitter ⚠
- p.Leu338Phe Single submitter ⚠
- p.Leu341Pro Single submitter ⚠
- p.Leu370Pro Single submitter ⚠
- p.Leu570Val Single submitter ⚠
- p.Lys167Arg Single submitter ⚠
- p.Lys594Thr Single submitter ⚠
- p.Met446Arg Single submitter ⚠
- p.Met497Ile Single submitter ⚠
- p.Met572Val Single submitter ⚠
- p.Met96Ile Single submitter ⚠
- p.Phe60Leu Single submitter ⚠
- p.Pro163Leu Single submitter ⚠
- p.Pro17His Single submitter ⚠
- p.Pro37Leu Single submitter ⚠
- p.Pro37Ser Single submitter ⚠
- p.Pro3Leu Single submitter ⚠
- p.Pro521Leu Single submitter ⚠
- p.Pro567Leu Single submitter ⚠
- p.Pro97Ala Single submitter ⚠
- p.Ser115Phe Single submitter ⚠
- p.Ser301Leu Single submitter ⚠
- p.Ser414Leu Single submitter ⚠
- p.Ser414Trp Single submitter ⚠
- p.Ser475Asn Single submitter ⚠
- p.Ser52Cys Single submitter ⚠
- p.Ser617Leu Single submitter ⚠
- p.Thr503Met Single submitter ⚠
- p.Thr55Ile Single submitter ⚠
- p.Trp593Cys Single submitter ⚠
- p.Tyr135Asn Single submitter ⚠
- p.Tyr179Cys Single submitter ⚠
- p.Tyr179His Single submitter ⚠
- p.Val166Leu Single submitter ⚠
- p.Val509Leu Single submitter ⚠
- p.Val509Met Single submitter ⚠
- p.Val543Met Single submitter ⚠
- p.Cys601fs No assertion criteria HAP1-related disorder
- p.His569fs No assertion criteria HAP1-related disorder