ATP6AP2 — 265 ClinVar variants

All ClinVar germline ATP6AP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 124 flagged for review →

5 Pathogenic · 1 Likely pathogenic · 13 Conflicting · 23 Benign · 5 Benign/Likely benign · 91 Likely benign · 127 Uncertain significance

Full ATP6AP2 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 agree, ClinVar conflicts 5

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

Predictors lean, ClinVar uncertain 60

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

Predictors split 59

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

All ATP6AP2 variants

Pathogenic 5

  • p.Asp107= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Ser95Ter Single submitter syndromic X-linked intellectual disability Hedera type
  • c.301-11_301-10del No assertion criteria syndromic X-linked intellectual disability Hedera type
  • p.Leu98Ser No assertion criteria congenital disorder of glycosylation, type IIr
  • p.Ser115= No assertion criteria X-linked parkinsonism-spasticity syndrome

Likely pathogenic 1

  • p.Asp210Tyr Single submitter syndromic X-linked intellectual disability Hedera type

Conflicting classifications of pathogenicity 13

  • c.534+7G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala286= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala64Thr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg152His Single submitter Inborn genetic diseases ⚠
  • p.Arg73Trp Single submitter Inborn genetic diseases ⚠
  • p.Asn308His Single submitter Inborn genetic diseases ⚠
  • p.Asn327Ser Single submitter Inborn genetic diseases ⚠
  • p.Asp180Gly Single submitter Inborn genetic diseases ⚠
  • p.Leu7Phe Single submitter Inborn genetic diseases ⚠
  • p.Met314Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro122Leu Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Thr75= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Val164Ile Single submitter Inborn genetic diseases ⚠

Benign 23

Benign/Likely benign 5

  • c.38-5T>C Multiple submitters syndromic X-linked intellectual disability Hedera type
  • c.534+10G>C Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Asp350= Multiple submitters congenital disorder of glycosylation, type IIr
  • p.Glu119= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Leu63= Multiple submitters History of neurodevelopmental disorder

Likely benign 91

  • c.300+19A>C Multiple submitters syndromic X-linked intellectual disability Hedera type
  • c.38-104G>A Multiple submitters
  • c.397-13A>G Multiple submitters syndromic X-linked intellectual disability Hedera type
  • c.534+8C>T Multiple submitters syndromic X-linked intellectual disability Hedera type
  • c.588+7A>G Multiple submitters syndromic X-linked intellectual disability Hedera type
  • c.859-11C>T Multiple submitters syndromic X-linked intellectual disability Hedera type
  • c.-120G>C Multiple submitters
  • c.-157T>C Multiple submitters
  • c.-224C>T Multiple submitters
  • c.-283G>T Multiple submitters
  • p.Ala74= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Arg133Lys Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asn17= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Glu40= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Ile274= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Leu158= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Phe144= Multiple submitters syndromic X-linked intellectual disability Hedera type
  • p.Ser172= Multiple submitters Inborn genetic diseases
  • c.168+15T>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.168+7A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.300+309G>C Single submitter
  • c.301-295G>A Single submitter
  • c.301-34A>T Single submitter
  • c.37+12G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.37+17C>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.38-13G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.396+18T>C Single submitter syndromic X-linked intellectual disability Hedera type
  • c.396+20T>C Single submitter
  • c.397-16T>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.397-9T>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.534+10G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.534+14T>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.534+16C>T Single submitter syndromic X-linked intellectual disability Hedera type
  • c.534+191C>A Single submitter
  • c.535-14dup Single submitter
  • c.535-14T>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.535-312G>A Single submitter
  • c.589-12T>C Single submitter syndromic X-linked intellectual disability Hedera type
  • c.589-19G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.589-6C>T Single submitter syndromic X-linked intellectual disability Hedera type
  • c.738+10A>T Single submitter syndromic X-linked intellectual disability Hedera type
  • c.738+11A>C Single submitter syndromic X-linked intellectual disability Hedera type
  • c.738+11A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.738+15G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.738+8T>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.739-5T>G Single submitter
  • c.859-11C>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.859-2A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.859-5T>C Single submitter syndromic X-linked intellectual disability Hedera type
  • c.859-9A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.-248A>T Single submitter
  • c.-36C>T Single submitter
  • p.Ala101= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala2= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala259= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala296= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala316= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala318= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala64= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ala9= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Arg155= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Arg234= Single submitter
  • p.Arg278= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Asn141= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Asn84= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Asp336= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Gln245= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ile315= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Leu106Ile Single submitter ⚠
  • p.Leu168= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Leu182= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Leu203= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Leu211= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Leu273= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Lys55= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Pro169= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Pro38= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser108= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser130= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser148= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser198= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser20= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser230= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Ser49= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Tyr226= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Tyr297= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Tyr340= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Val11= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Val124= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Val137= Single submitter syndromic X-linked intellectual disability Hedera type
  • p.Val310= Single submitter syndromic X-linked intellectual disability Hedera type

Uncertain significance 127

  • p.Ala259Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Arg155Cys Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg199His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg41Gln Multiple submitters congenital disorder of glycosylation, type IIr ⚠
  • p.Asn17Ser Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asp242Asn Multiple submitters Inborn genetic diseases ⚠
  • p.Gly16Glu Multiple submitters ATP6AP2-related disorder ⚠
  • p.Gly33Glu Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • p.Leu125Phe Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ser167Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Ser53Phe Multiple submitters ATP6AP2-related disorder ⚠
  • p.Ser92Asn Multiple submitters ATP6AP2-related disorder ⚠
  • p.Tyr293Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Val54Leu Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val78Leu Multiple submitters syndromic X-linked intellectual disability Hedera type ⚠
  • c.168+3A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.168+6T>A Single submitter Inborn genetic diseases
  • c.300+4A>G Single submitter
  • c.37+5G>A Single submitter syndromic X-linked intellectual disability Hedera type
  • c.38-8C>G Single submitter
  • c.534+55A>G Single submitter
  • c.535-11dup Single submitter
  • c.588+4A>G Single submitter
  • c.589-3A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.739-5_739-4del Single submitter syndromic X-linked intellectual disability Hedera type
  • c.739-7C>A Single submitter
  • c.858+4A>G Single submitter syndromic X-linked intellectual disability Hedera type
  • c.-70C>T Single submitter
  • c.*640A>G Single submitter
  • p.Ala110Thr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala128Pro Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala128Val Single submitter ⚠
  • p.Ala12Val Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala217Glu Single submitter Inborn genetic diseases ⚠
  • p.Ala236Gly Single submitter Inborn genetic diseases ⚠
  • p.Ala243Thr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala286Val Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala316Thr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala318Asp Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ala87Pro Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg152Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg155Gly Single submitter ⚠
  • p.Arg155His Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg157Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg199Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg225Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg225His Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg278Gly Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg31Gln Single submitter ⚠
  • p.Arg341Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg41Trp Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg71Cys Single submitter ⚠
  • p.Arg71His Single submitter congenital disorder of glycosylation, type IIr ⚠
  • p.Arg73Gln Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Arg73Gly Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asn177Asp Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asn177Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asn327Asp Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asp206Glu Single submitter ⚠
  • p.Asp210Gly Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Asp249Gly Single submitter ⚠
  • p.Asp57Asn Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Gln245Arg Single submitter ⚠
  • p.Glu18Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu231Val Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Glu56Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu99Lys Single submitter ⚠
  • p.Gly256Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.His114Tyr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.His70Leu Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ile21Met Single submitter ⚠
  • p.Ile222Met Single submitter ⚠
  • p.Ile280Met Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ile280Val Single submitter ⚠
  • p.Ile322Phe Single submitter ⚠
  • p.Ile323Val Single submitter ⚠
  • p.Ile339Thr Single submitter ⚠
  • p.Ile339Val Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Leu10Phe Single submitter ⚠
  • p.Leu151Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Leu170Ile Single submitter ⚠
  • p.Leu196= Single submitter
  • p.Leu22Phe Single submitter ⚠
  • p.Leu273Phe Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Leu273Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu281Phe Single submitter ⚠
  • p.Leu88Val Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Lys205Asn Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Met136Ile Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Met136Thr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Met251Thr Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Met314Ile Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Met331Val Single submitter ⚠
  • p.Phe117Leu Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Pro122His Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Pro129Ala Single submitter ⚠
  • p.Pro36Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Pro43Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Pro89Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Pro97Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ser105Arg Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ser108Asn Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ser166Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ser185Cys Single submitter ⚠
  • p.Ser208Pro Single submitter ⚠
  • p.Ser337Arg Single submitter ⚠
  • p.Ser59Cys Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Ser95Leu Single submitter ⚠
  • p.Thr150Ile Single submitter ⚠
  • p.Thr150Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Thr271Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Thr279Ala Single submitter ⚠
  • p.Thr343Arg Single submitter congenital disorder of glycosylation, type IIr ⚠
  • p.Tyr255His Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Tyr293Ser Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Tyr96Phe Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val109Leu Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val11Ala Single submitter ⚠
  • p.Val143Ala Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val149Phe Single submitter ⚠
  • p.Val179Ala Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val189Met Single submitter Inborn genetic diseases ⚠
  • p.Val260Met Single submitter ⚠
  • p.Val305Met Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val321Met Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val76Ile Single submitter syndromic X-linked intellectual disability Hedera type ⚠
  • p.Val80Leu Single submitter ⚠