ATP4A — 262 ClinVar variants
All ClinVar germline ATP4A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 169 flagged for review →
36 Benign · 56 Likely benign · 170 Uncertain significance
Full ATP4A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 169
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 121
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- ATP4A p.Ala104Val Uncertain significance Multiple submitters
- ATP4A p.Ala119Thr Uncertain significance Multiple submitters
- ATP4A p.Ala170Ser Uncertain significance Multiple submitters
- ATP4A p.Arg607Trp Uncertain significance Multiple submitters
- ATP4A p.Arg660His Uncertain significance Multiple submitters
- ATP4A p.Arg703Cys Uncertain significance Multiple submitters
- ATP4A p.Arg951Cys Uncertain significance Multiple submitters
- ATP4A p.Asp139Asn Uncertain significance Multiple submitters
- ATP4A p.Asp200Asn Uncertain significance Multiple submitters
- ATP4A p.Gly558Asp Uncertain significance Multiple submitters
- ATP4A p.Gly727Arg Uncertain significance Multiple submitters
- ATP4A p.Ile311Val Uncertain significance Multiple submitters
- ATP4A p.Ile457Asn Uncertain significance Multiple submitters
- ATP4A p.Ile995Val Uncertain significance Multiple submitters
- ATP4A p.Thr505Lys Uncertain significance Multiple submitters
- ATP4A p.Val12Met Uncertain significance Multiple submitters
- ATP4A p.Val700Leu Uncertain significance Multiple submitters
- ATP4A p.Ala218Val Uncertain significance Single submitter
- ATP4A p.Ala285Val Uncertain significance Single submitter
- ATP4A p.Ala307Thr Uncertain significance Single submitter
- ATP4A p.Ala307Val Uncertain significance Single submitter
- ATP4A p.Ala32Glu Uncertain significance Single submitter
- ATP4A p.Ala359Thr Uncertain significance Single submitter
- ATP4A p.Ala411Asp Uncertain significance Single submitter
- ATP4A p.Ala597Val Uncertain significance Single submitter
- ATP4A p.Ala620Thr Uncertain significance Single submitter
- ATP4A p.Ala721Val Uncertain significance Single submitter
- ATP4A p.Arg1022His Uncertain significance Single submitter
- ATP4A p.Arg184His Uncertain significance Single submitter
- ATP4A p.Arg215Cys Uncertain significance Single submitter
- ATP4A p.Arg238Cys Uncertain significance Single submitter
- ATP4A p.Arg238His Uncertain significance Single submitter
- ATP4A p.Arg280Gly Uncertain significance Single submitter
- ATP4A p.Arg396Cys Uncertain significance Single submitter
- ATP4A p.Arg482Gln Uncertain significance Single submitter
- ATP4A p.Arg510Gln Uncertain significance Single submitter
- ATP4A p.Arg524Ser Uncertain significance Single submitter
- ATP4A p.Arg607Gln Uncertain significance Single submitter
- ATP4A p.Arg618Cys Uncertain significance Single submitter
- ATP4A p.Arg660Cys Uncertain significance Single submitter
- ATP4A p.Arg668His Uncertain significance Single submitter
- ATP4A p.Arg668Leu Uncertain significance Single submitter
- ATP4A p.Arg694His Uncertain significance Single submitter
- ATP4A p.Arg718Trp Uncertain significance Single submitter
- ATP4A p.Arg777Gln Uncertain significance Single submitter
- ATP4A p.Arg848Cys Uncertain significance Single submitter
- ATP4A p.Arg922Cys Uncertain significance Single submitter
- ATP4A p.Arg95Gln Uncertain significance Single submitter
- ATP4A p.Asn371Asp Uncertain significance Single submitter
- ATP4A p.Asn494Asp Uncertain significance Single submitter
- ATP4A p.Asp200Glu Uncertain significance Single submitter
- ATP4A p.Asp274His Uncertain significance Single submitter
- ATP4A p.Asp508Asn Uncertain significance Single submitter
- ATP4A p.Asp751His Uncertain significance Single submitter
- ATP4A p.Asp944Asn Uncertain significance Single submitter
- ATP4A p.Asp944Glu Uncertain significance Single submitter
- ATP4A p.Cys529Arg Uncertain significance Single submitter
- ATP4A p.Cys981Tyr Uncertain significance Single submitter
- ATP4A p.Gln220Arg Uncertain significance Single submitter
- ATP4A p.Gln448His Uncertain significance Single submitter
- ATP4A p.Gln717Leu Uncertain significance Single submitter
- ATP4A p.Glu249Lys Uncertain significance Single submitter
- ATP4A p.Glu472Asp Uncertain significance Single submitter
- ATP4A p.Glu523Gly Uncertain significance Single submitter
- ATP4A p.Glu650Lys Uncertain significance Single submitter
- ATP4A p.Glu99Asp Uncertain significance Single submitter
- ATP4A p.Gly1007Ser Uncertain significance Single submitter
- ATP4A p.Gly155Arg Uncertain significance Single submitter
- ATP4A p.Gly158Val Uncertain significance Single submitter
- ATP4A p.Gly19Ser Uncertain significance Single submitter
- ATP4A p.Gly287Arg Uncertain significance Single submitter
- ATP4A p.Gly36Asp Uncertain significance Single submitter
- ATP4A p.Gly742Arg Uncertain significance Single submitter
- ATP4A p.Gly814Arg Uncertain significance Single submitter
- ATP4A p.Gly959Ala Uncertain significance Single submitter
- ATP4A p.Gly977Arg Uncertain significance Single submitter
- ATP4A p.His55Pro Uncertain significance Single submitter
- ATP4A p.His844Arg Uncertain significance Single submitter
- ATP4A p.Ile148Thr Uncertain significance Single submitter
- ATP4A p.Ile169Val Uncertain significance Single submitter
- ATP4A p.Ile52Thr Uncertain significance Single submitter
- ATP4A p.Ile787Thr Uncertain significance Single submitter
- ATP4A p.Leu946Val Uncertain significance Single submitter
- ATP4A p.Lys487Asn Uncertain significance Single submitter
- ATP4A p.Lys535Arg Uncertain significance Single submitter
- ATP4A p.Met397Val Uncertain significance Single submitter
- ATP4A p.Met50Leu Uncertain significance Single submitter
- ATP4A p.Met587Thr Uncertain significance Single submitter
- ATP4A p.Met602Val Uncertain significance Single submitter
- ATP4A p.Met843Thr Uncertain significance Single submitter
- ATP4A p.Phe566Cys Uncertain significance Single submitter
- ATP4A p.Phe881Leu Uncertain significance Single submitter
- ATP4A p.Pro247Ser Uncertain significance Single submitter
- ATP4A p.Pro454Ser Uncertain significance Single submitter
- ATP4A p.Pro486Thr Uncertain significance Single submitter
- ATP4A p.Pro578Arg Uncertain significance Single submitter
- ATP4A p.Pro94Leu Uncertain significance Single submitter
- ATP4A p.Ser228Leu Uncertain significance Single submitter
- ATP4A p.Ser283Leu Uncertain significance Single submitter
- ATP4A p.Ser386Trp Uncertain significance Single submitter
- ATP4A p.Ser425Thr Uncertain significance Single submitter
- ATP4A p.Ser687Leu Uncertain significance Single submitter
- ATP4A p.Ser687Thr Uncertain significance Single submitter
- ATP4A p.Ser77Gly Uncertain significance Single submitter
- ATP4A p.Ser936Ile Uncertain significance Single submitter
- ATP4A p.Ser954Cys Uncertain significance Single submitter
- ATP4A p.Thr276Ala Uncertain significance Single submitter
- ATP4A p.Thr327Ser Uncertain significance Single submitter
- ATP4A p.Thr726Met Uncertain significance Single submitter
- ATP4A p.Thr882Met Uncertain significance Single submitter
- ATP4A p.Trp116Cys Uncertain significance Single submitter
- ATP4A p.Val1002Ala Uncertain significance Single submitter
- ATP4A p.Val101Ile Uncertain significance Single submitter
- ATP4A p.Val1021Ala Uncertain significance Single submitter
- ATP4A p.Val153Ile Uncertain significance Single submitter
- ATP4A p.Val265Leu Uncertain significance Single submitter
- ATP4A p.Val339Met Uncertain significance Single submitter
- ATP4A p.Val610Ile Uncertain significance Single submitter
- ATP4A p.Val700Ala Uncertain significance Single submitter
- ATP4A p.Val807Ile Uncertain significance Single submitter
- ATP4A p.Val895Met Uncertain significance Single submitter
Predictors split 48
The independent predictors disagree with each other — read with care.
- ATP4A p.Ala104Thr Uncertain significance Multiple submitters
- ATP4A p.Ala90Thr Uncertain significance Multiple submitters
- ATP4A p.Arg668Cys Uncertain significance Multiple submitters
- ATP4A p.Arg852His Uncertain significance Multiple submitters
- ATP4A p.Gln680Leu Likely benign Multiple submitters
- ATP4A p.Glu300Lys Uncertain significance Multiple submitters
- ATP4A p.Gly419Glu Uncertain significance Multiple submitters
- ATP4A p.Pro240His Benign Multiple submitters
- ATP4A p.Ser530Asn Likely benign Multiple submitters
- ATP4A p.Thr243Met Uncertain significance Multiple submitters
- ATP4A p.Tyr553Cys Uncertain significance Multiple submitters
- ATP4A p.Ala120Thr Uncertain significance Single submitter
- ATP4A p.Ala193Thr Uncertain significance Single submitter
- ATP4A p.Ala307Gly Uncertain significance Single submitter
- ATP4A p.Ala431Glu Uncertain significance Single submitter
- ATP4A p.Ala552Thr Uncertain significance Single submitter
- ATP4A p.Ala748Thr Uncertain significance Single submitter
- ATP4A p.Ala943Thr Uncertain significance Single submitter
- ATP4A p.Arg330Trp Uncertain significance Single submitter
- ATP4A p.Arg672Cys Uncertain significance Single submitter
- ATP4A p.Arg846Cys Uncertain significance Single submitter
- ATP4A p.Arg85Gln Uncertain significance Single submitter
- ATP4A p.Arg92Trp Uncertain significance Single submitter
- ATP4A p.Arg95Trp Uncertain significance Single submitter
- ATP4A p.Asn497Thr Uncertain significance Single submitter
- ATP4A p.Asp416Gly Uncertain significance Single submitter
- ATP4A p.Asp583Asn Uncertain significance Single submitter
- ATP4A p.Cys323Gly Uncertain significance Single submitter
- ATP4A p.Gln178Pro Uncertain significance Single submitter
- ATP4A p.Gln910Pro Uncertain significance Single submitter
- ATP4A p.Glu289Gly Uncertain significance Single submitter
- ATP4A p.Glu691Lys Uncertain significance Single submitter
- ATP4A p.Gly593Ser Uncertain significance Single submitter
- ATP4A p.Gly985Ser Uncertain significance Single submitter
- ATP4A p.Ile319Thr Uncertain significance Single submitter
- ATP4A p.Ile787Val Uncertain significance Single submitter
- ATP4A p.Lys738Arg Uncertain significance Single submitter
- ATP4A p.Phe866Leu Uncertain significance Single submitter
- ATP4A p.Ser286Leu Uncertain significance Single submitter
- ATP4A p.Ser426Leu Uncertain significance Single submitter
- ATP4A p.Thr237Ile Uncertain significance Single submitter
- ATP4A p.Thr465Met Uncertain significance Single submitter
- ATP4A p.Thr97Ala Uncertain significance Single submitter
- ATP4A p.Tyr160His Uncertain significance Single submitter
- ATP4A p.Val117Gly Uncertain significance Single submitter
- ATP4A p.Val451Leu Uncertain significance Single submitter
- ATP4A p.Val809Met Uncertain significance Single submitter
- ATP4A p.Val971Met Uncertain significance Single submitter
All ATP4A variants
Benign 36
- c.1500+5G>T Multiple submitters
- c.2006+11C>A Multiple submitters
- c.788-19C>T Multiple submitters
- p.Asn53= Multiple submitters
- p.Ile145= Multiple submitters
- p.Ile503= Multiple submitters
- p.Phe103= Multiple submitters
- p.Pro240His Multiple submitters ⚠
- p.Pro810= Multiple submitters
- p.Thr619= Multiple submitters
- p.Val265Ala Multiple submitters
- p.Val584= Multiple submitters
- c.1501-11C>A Single submitter
- c.1501-15C>T Single submitter
- c.1501-9dup Single submitter
- c.157-14A>G Single submitter
- c.217-20G>A Single submitter
- c.2482-12A>G Single submitter
- c.2752-19G>A Single submitter
- c.2885+16C>T Single submitter
- c.535-17G>A Single submitter
- p.Arg898= Single submitter
- p.Asn174= Single submitter
- p.Asn371= Single submitter
- p.Asn89= Single submitter
- p.Gly476= Single submitter
- p.Gly560= Single submitter
- p.Ile1010= Single submitter
- p.Ile457= Single submitter
- p.Leu980= Single submitter
- p.Phe780= Single submitter
- p.Pro662= Single submitter
- p.Pro697= Single submitter
- p.Tyr100= Single submitter
- p.Tyr913= Single submitter
- p.Val690= Single submitter
Likely benign 56
- p.Gln680Leu Multiple submitters ⚠
- p.Ser530Asn Multiple submitters ⚠
- p.Thr264= Multiple submitters
- c.1056+16C>T Single submitter
- c.1056+7G>A Single submitter
- c.1365+11G>C Single submitter
- c.1501-11C>G Single submitter
- c.1501-11C>T Single submitter
- c.1501-14C>T Single submitter
- c.1501-19C>T Single submitter
- c.157-12C>T Single submitter
- c.1693+7C>G Single submitter
- c.2006+17C>T Single submitter
- c.216+20C>T Single submitter
- c.2327-5C>T Single submitter
- c.2605+11G>A Single submitter
- c.2605+18G>A Single submitter
- c.2751+15G>A Single submitter
- c.2885+20T>C Single submitter
- c.2886-6C>T Single submitter
- c.3080-17C>T Single submitter
- c.420+9T>C Single submitter
- p.Ala119= Single submitter
- p.Ala212= Single submitter
- p.Ala60= Single submitter
- p.Ala702= Single submitter
- p.Ala943= Single submitter
- p.Arg184= Single submitter
- p.Asp194Glu Single submitter
- p.Asp542= Single submitter
- p.Gly985= Single submitter
- p.His905Asn Single submitter
- p.Ile169= Single submitter
- p.Ile299= Single submitter
- p.Ile633= Single submitter
- p.Ile655= Single submitter
- p.Ile741= Single submitter
- p.Leu201= Single submitter
- p.Leu559= Single submitter
- p.Leu783= Single submitter
- p.Lys709= Single submitter
- p.Pro88= Single submitter
- p.Ser649= Single submitter
- p.Ser687= Single submitter
- p.Thr137= Single submitter
- p.Thr272= Single submitter
- p.Thr350= Single submitter
- p.Thr496Pro Single submitter
- p.Thr551= Single submitter
- p.Thr628= Single submitter
- p.Thr792= Single submitter
- p.Thr806= Single submitter
- p.Thr882= Single submitter
- p.Tyr1006= Single submitter
- p.Tyr142= Single submitter
- p.Val453= Single submitter
Uncertain significance 170
- p.Ala104Thr Multiple submitters ⚠
- p.Ala104Val Multiple submitters ⚠
- p.Ala119Thr Multiple submitters ⚠
- p.Ala170Ser Multiple submitters ⚠
- p.Ala90Thr Multiple submitters ⚠
- p.Arg607Trp Multiple submitters ⚠
- p.Arg660His Multiple submitters ⚠
- p.Arg668Cys Multiple submitters ⚠
- p.Arg703Cys Multiple submitters ⚠
- p.Arg852His Multiple submitters ⚠
- p.Arg951Cys Multiple submitters ⚠
- p.Asp139Asn Multiple submitters ⚠
- p.Asp200Asn Multiple submitters ⚠
- p.Glu300Lys Multiple submitters ⚠
- p.Gly419Glu Multiple submitters ⚠
- p.Gly558Asp Multiple submitters ⚠
- p.Gly727Arg Multiple submitters ⚠
- p.Ile311Val Multiple submitters ⚠
- p.Ile457Asn Multiple submitters ⚠
- p.Ile995Val Multiple submitters ⚠
- p.Thr243Met Multiple submitters ⚠
- p.Thr505Lys Multiple submitters ⚠
- p.Tyr553Cys Multiple submitters ⚠
- p.Val12Met Multiple submitters ⚠
- p.Val700Leu Multiple submitters ⚠
- c.1501-10C>G Single submitter
- c.2326+4C>T Single submitter
- p.Ala120Thr Single submitter ⚠
- p.Ala193Thr Single submitter ⚠
- p.Ala218Val Single submitter ⚠
- p.Ala285Val Single submitter ⚠
- p.Ala307Gly Single submitter ⚠
- p.Ala307Thr Single submitter ⚠
- p.Ala307Val Single submitter ⚠
- p.Ala32Glu Single submitter ⚠
- p.Ala359Thr Single submitter ⚠
- p.Ala411Asp Single submitter ⚠
- p.Ala431Glu Single submitter ⚠
- p.Ala552Thr Single submitter ⚠
- p.Ala597Val Single submitter ⚠
- p.Ala620Thr Single submitter ⚠
- p.Ala721Val Single submitter ⚠
- p.Ala748Thr Single submitter ⚠
- p.Ala943Thr Single submitter ⚠
- p.Arg1022His Single submitter ⚠
- p.Arg184His Single submitter ⚠
- p.Arg215Cys Single submitter ⚠
- p.Arg238Cys Single submitter ⚠
- p.Arg238His Single submitter ⚠
- p.Arg280Gly Single submitter ⚠
- p.Arg330Trp Single submitter ⚠
- p.Arg396Cys Single submitter ⚠
- p.Arg482Gln Single submitter ⚠
- p.Arg510Gln Single submitter ⚠
- p.Arg524Ser Single submitter ⚠
- p.Arg607Gln Single submitter ⚠
- p.Arg618Cys Single submitter ⚠
- p.Arg660Cys Single submitter ⚠
- p.Arg668His Single submitter ⚠
- p.Arg668Leu Single submitter ⚠
- p.Arg672Cys Single submitter ⚠
- p.Arg694His Single submitter ⚠
- p.Arg718Trp Single submitter ⚠
- p.Arg777Gln Single submitter ⚠
- p.Arg846Cys Single submitter ⚠
- p.Arg848Cys Single submitter ⚠
- p.Arg85Gln Single submitter ⚠
- p.Arg922Cys Single submitter ⚠
- p.Arg92Trp Single submitter ⚠
- p.Arg95Gln Single submitter ⚠
- p.Arg95Trp Single submitter ⚠
- p.Asn371Asp Single submitter ⚠
- p.Asn494Asp Single submitter ⚠
- p.Asn497Thr Single submitter ⚠
- p.Asp200Glu Single submitter ⚠
- p.Asp274His Single submitter ⚠
- p.Asp416Gly Single submitter ⚠
- p.Asp508Asn Single submitter ⚠
- p.Asp583Asn Single submitter ⚠
- p.Asp751His Single submitter ⚠
- p.Asp944Asn Single submitter ⚠
- p.Asp944Glu Single submitter ⚠
- p.Cys323Gly Single submitter ⚠
- p.Cys529Arg Single submitter ⚠
- p.Cys981Tyr Single submitter ⚠
- p.Gln178Pro Single submitter ⚠
- p.Gln220Arg Single submitter ⚠
- p.Gln424fs Single submitter
- p.Gln448His Single submitter ⚠
- p.Gln717Leu Single submitter ⚠
- p.Gln910Pro Single submitter ⚠
- p.Glu249Lys Single submitter ⚠
- p.Glu289Gly Single submitter ⚠
- p.Glu472Asp Single submitter ⚠
- p.Glu523Gly Single submitter ⚠
- p.Glu650Lys Single submitter ⚠
- p.Glu691Lys Single submitter ⚠
- p.Glu99Asp Single submitter ⚠
- p.Gly1007Ser Single submitter ⚠
- p.Gly155Arg Single submitter ⚠
- p.Gly158Val Single submitter ⚠
- p.Gly19Ser Single submitter ⚠
- p.Gly287Arg Single submitter ⚠
- p.Gly36Asp Single submitter ⚠
- p.Gly593Ser Single submitter ⚠
- p.Gly742Arg Single submitter ⚠
- p.Gly814Arg Single submitter ⚠
- p.Gly959Ala Single submitter ⚠
- p.Gly977Arg Single submitter ⚠
- p.Gly985Ser Single submitter ⚠
- p.His55Pro Single submitter ⚠
- p.His844Arg Single submitter ⚠
- p.Ile148Thr Single submitter ⚠
- p.Ile169Val Single submitter ⚠
- p.Ile319Thr Single submitter ⚠
- p.Ile52Thr Single submitter ⚠
- p.Ile787Thr Single submitter ⚠
- p.Ile787Val Single submitter ⚠
- p.Leu946Val Single submitter ⚠
- p.Lys487Asn Single submitter ⚠
- p.Lys535Arg Single submitter ⚠
- p.Lys738Arg Single submitter ⚠
- p.Met397Val Single submitter ⚠
- p.Met50Leu Single submitter ⚠
- p.Met587Thr Single submitter ⚠
- p.Met602Val Single submitter ⚠
- p.Met843Thr Single submitter ⚠
- p.Phe566Cys Single submitter ⚠
- p.Phe866Leu Single submitter ⚠
- p.Phe881Leu Single submitter ⚠
- p.Pro247Ser Single submitter ⚠
- p.Pro454Ser Single submitter ⚠
- p.Pro486Thr Single submitter ⚠
- p.Pro578Arg Single submitter ⚠
- p.Pro94Leu Single submitter ⚠
- p.Ser228Leu Single submitter ⚠
- p.Ser283_Leu284= Single submitter
- p.Ser283Leu Single submitter ⚠
- p.Ser286Leu Single submitter ⚠
- p.Ser386Trp Single submitter ⚠
- p.Ser425Thr Single submitter ⚠
- p.Ser426Leu Single submitter ⚠
- p.Ser687Leu Single submitter ⚠
- p.Ser687Thr Single submitter ⚠
- p.Ser77Gly Single submitter ⚠
- p.Ser936Ile Single submitter ⚠
- p.Ser954Cys Single submitter ⚠
- p.Thr237Ile Single submitter ⚠
- p.Thr276Ala Single submitter ⚠
- p.Thr327Ser Single submitter ⚠
- p.Thr465Met Single submitter ⚠
- p.Thr726Met Single submitter ⚠
- p.Thr882Met Single submitter ⚠
- p.Thr97Ala Single submitter ⚠
- p.Trp116Cys Single submitter ⚠
- p.Tyr160His Single submitter ⚠
- p.Val1002Ala Single submitter ⚠
- p.Val101Ile Single submitter ⚠
- p.Val1021Ala Single submitter ⚠
- p.Val117Gly Single submitter ⚠
- p.Val153Ile Single submitter ⚠
- p.Val265Leu Single submitter ⚠
- p.Val339Met Single submitter ⚠
- p.Val451Leu Single submitter ⚠
- p.Val610Ile Single submitter ⚠
- p.Val700Ala Single submitter ⚠
- p.Val807Ile Single submitter ⚠
- p.Val809Met Single submitter ⚠
- p.Val895Met Single submitter ⚠
- p.Val971Met Single submitter ⚠