ATP2A3 — 192 ClinVar variants
All ClinVar germline ATP2A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 140 flagged for review →
2 Conflicting · 24 Benign · 2 Benign/Likely benign · 32 Likely benign · 132 Uncertain significance
Full ATP2A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 140
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 54
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- ATP2A3 p.Ala112Thr Uncertain significance Single submitter
- ATP2A3 p.Ala219Val Uncertain significance Single submitter
- ATP2A3 p.Ala3Val Uncertain significance Single submitter
- ATP2A3 p.Ala569Thr Uncertain significance Single submitter
- ATP2A3 p.Ala608Pro Uncertain significance Single submitter
- ATP2A3 p.Ala617Val Uncertain significance Single submitter
- ATP2A3 p.Ala649Thr Uncertain significance Single submitter
- ATP2A3 p.Ala652Pro Uncertain significance Single submitter
- ATP2A3 p.Ala677Thr Uncertain significance Single submitter
- ATP2A3 p.Arg131His Uncertain significance Single submitter
- ATP2A3 p.Arg134His Uncertain significance Single submitter
- ATP2A3 p.Arg164Cys Uncertain significance Single submitter
- ATP2A3 p.Arg480Gln Uncertain significance Single submitter
- ATP2A3 p.Arg529His Uncertain significance Single submitter
- ATP2A3 p.Arg550Gln Uncertain significance Single submitter
- ATP2A3 p.Arg762His Uncertain significance Single submitter
- ATP2A3 p.Arg822Gln Uncertain significance Single submitter
- ATP2A3 p.Arg965His Uncertain significance Single submitter
- ATP2A3 p.Asn101Asp Uncertain significance Single submitter
- ATP2A3 p.Asn275Thr Uncertain significance Single submitter
- ATP2A3 p.Asn330Lys Uncertain significance Single submitter
- ATP2A3 p.Asp11Glu Uncertain significance Single submitter
- ATP2A3 p.Asp176Asn Uncertain significance Single submitter
- ATP2A3 p.Cys581Ser Uncertain significance Single submitter
- ATP2A3 p.Glu109Gly Uncertain significance Single submitter
- ATP2A3 p.Glu878Lys Uncertain significance Single submitter
- ATP2A3 p.Glu994Gly Uncertain significance Single submitter
- ATP2A3 p.Gly405Ser Uncertain significance Single submitter
- ATP2A3 p.Gly845Ser Uncertain significance Single submitter
- ATP2A3 p.Ile194Val Uncertain significance Single submitter
- ATP2A3 p.Leu311Ile Uncertain significance Single submitter
- ATP2A3 p.Leu41Pro Uncertain significance Single submitter
- ATP2A3 p.Met239Thr Uncertain significance Single submitter
- ATP2A3 p.Met452Ile Uncertain significance Single submitter
- ATP2A3 p.Met996Val Uncertain significance Single submitter
- ATP2A3 p.Phe57Ser Uncertain significance Single submitter
- ATP2A3 p.Pro124Thr Uncertain significance Single submitter
- ATP2A3 p.Pro312Leu Uncertain significance Single submitter
- ATP2A3 p.Pro391Arg Uncertain significance Single submitter
- ATP2A3 p.Pro602Leu Uncertain significance Single submitter
- ATP2A3 p.Ser170Tyr Uncertain significance Single submitter
- ATP2A3 p.Ser526Thr Uncertain significance Single submitter
- ATP2A3 p.Ser917Leu Uncertain significance Single submitter
- ATP2A3 p.Thr172Lys Uncertain significance Single submitter
- ATP2A3 p.Thr390Asn Uncertain significance Single submitter
- ATP2A3 p.Thr441Met Uncertain significance Single submitter
- ATP2A3 p.Thr724Met Uncertain significance Single submitter
- ATP2A3 p.Tyr754Cys Uncertain significance Single submitter
- ATP2A3 p.Val106Glu Uncertain significance Single submitter
- ATP2A3 p.Val200Met Uncertain significance Single submitter
- ATP2A3 p.Val271Met Uncertain significance Single submitter
- ATP2A3 p.Val300Met Uncertain significance Single submitter
- ATP2A3 p.Val339Met Uncertain significance Single submitter
- ATP2A3 p.Val679Met Uncertain significance Single submitter
Predictors split 86
The independent predictors disagree with each other — read with care.
- ATP2A3 p.Arg674Cys Likely benign Multiple submitters
- ATP2A3 p.Ala327Ser Uncertain significance Single submitter
- ATP2A3 p.Ala32Gly Uncertain significance Single submitter
- ATP2A3 p.Ala372Asp Uncertain significance Single submitter
- ATP2A3 p.Ala418Ser Uncertain significance Single submitter
- ATP2A3 p.Ala4Ser Uncertain significance Single submitter
- ATP2A3 p.Ala569Val Likely benign Single submitter
- ATP2A3 p.Ala673Thr Uncertain significance Single submitter
- ATP2A3 p.Ala745Thr Uncertain significance Single submitter
- ATP2A3 p.Ala912Ser Uncertain significance Single submitter
- ATP2A3 p.Arg110His Uncertain significance Single submitter
- ATP2A3 p.Arg141Cys Uncertain significance Single submitter
- ATP2A3 p.Arg143Gln Uncertain significance Single submitter
- ATP2A3 p.Arg143Trp Uncertain significance Single submitter
- ATP2A3 p.Arg324Gln Uncertain significance Single submitter
- ATP2A3 p.Arg324Trp Uncertain significance Single submitter
- ATP2A3 p.Arg325Cys Uncertain significance Single submitter
- ATP2A3 p.Arg328Cys Uncertain significance Single submitter
- ATP2A3 p.Arg33Gln Uncertain significance Single submitter
- ATP2A3 p.Arg464Trp Uncertain significance Single submitter
- ATP2A3 p.Arg467Gln Uncertain significance Single submitter
- ATP2A3 p.Arg572Lys Uncertain significance Single submitter
- ATP2A3 p.Arg613Cys Uncertain significance Single submitter
- ATP2A3 p.Arg613His Uncertain significance Single submitter
- ATP2A3 p.Arg637Cys Uncertain significance Single submitter
- ATP2A3 p.Arg63Cys Uncertain significance Single submitter
- ATP2A3 p.Arg686Cys Uncertain significance Single submitter
- ATP2A3 p.Arg686His Uncertain significance Single submitter
- ATP2A3 p.Arg825Gly Uncertain significance Single submitter
- ATP2A3 p.Arg924Trp Conflicting Single submitter
- ATP2A3 p.Asp399Asn Uncertain significance Single submitter
- ATP2A3 p.Asp580Asn Uncertain significance Single submitter
- ATP2A3 p.Cys581Tyr Uncertain significance Single submitter
- ATP2A3 p.Gln616Glu Uncertain significance Single submitter
- ATP2A3 p.Glu21Lys Uncertain significance Single submitter
- ATP2A3 p.Glu243Lys Uncertain significance Single submitter
- ATP2A3 p.Glu245Gln Uncertain significance Single submitter
- ATP2A3 p.Glu381Gly Uncertain significance Single submitter
- ATP2A3 p.Glu45Asp Uncertain significance Single submitter
- ATP2A3 p.Glu664Gln Uncertain significance Single submitter
- ATP2A3 p.Glu664Lys Uncertain significance Single submitter
- ATP2A3 p.Glu82Lys Uncertain significance Single submitter
- ATP2A3 p.Glu892Gly Uncertain significance Single submitter
- ATP2A3 p.Gly227Ser Uncertain significance Single submitter
- ATP2A3 p.Gly398Arg Uncertain significance Single submitter
- ATP2A3 p.Gly630Val Uncertain significance Single submitter
- ATP2A3 p.Gly885Ser Uncertain significance Single submitter
- ATP2A3 p.Gly964Arg Uncertain significance Single submitter
- ATP2A3 p.Ile145Val Uncertain significance Single submitter
- ATP2A3 p.Ile816Val Uncertain significance Single submitter
- ATP2A3 p.Ile907Thr Uncertain significance Single submitter
- ATP2A3 p.Leu7Phe Uncertain significance Single submitter
- ATP2A3 p.Leu913Phe Uncertain significance Single submitter
- ATP2A3 p.Leu962Val Uncertain significance Single submitter
- ATP2A3 p.Met733Val Uncertain significance Single submitter
- ATP2A3 p.Pro26Leu Uncertain significance Single submitter
- ATP2A3 p.Pro282Leu Uncertain significance Single submitter
- ATP2A3 p.Pro500Ser Uncertain significance Single submitter
- ATP2A3 p.Pro505Leu Conflicting Single submitter
- ATP2A3 p.Pro536Ser Uncertain significance Single submitter
- ATP2A3 p.Pro824Ser Uncertain significance Single submitter
- ATP2A3 p.Pro881Ala Uncertain significance Single submitter
- ATP2A3 p.Pro881Leu Uncertain significance Single submitter
- ATP2A3 p.Ser216Leu Uncertain significance Single submitter
- ATP2A3 p.Thr230Ser Uncertain significance Single submitter
- ATP2A3 p.Thr390Ile Uncertain significance Single submitter
- ATP2A3 p.Thr654Met Uncertain significance Single submitter
- ATP2A3 p.Tyr986His Uncertain significance Single submitter
- ATP2A3 p.Val106Met Uncertain significance Single submitter
- ATP2A3 p.Val137Met Uncertain significance Single submitter
- ATP2A3 p.Val185Met Uncertain significance Single submitter
- ATP2A3 p.Val224Met Uncertain significance Single submitter
- ATP2A3 p.Val269Met Uncertain significance Single submitter
- ATP2A3 p.Val597Ile Uncertain significance Single submitter
- ATP2A3 p.Val773Ile Uncertain significance Single submitter
- ATP2A3 p.Val842Gly Uncertain significance Single submitter
- ATP2A3 p.Val890Met Uncertain significance Single submitter
- ATP2A3 p.Val89Ala Uncertain significance Single submitter
- ATP2A3 p.Val89Met Uncertain significance Single submitter
- ATP2A3 p.Val916Ile Uncertain significance Single submitter
- ATP2A3 p.Val950Met Uncertain significance Single submitter
- ATP2A3 p.Val959Met Uncertain significance Single submitter
-
ATP2A3 p.Ala745Asp
Likely benign
No assertion criteria
ATP2A3-related disorder
-
ATP2A3 p.Arg674His
Benign
No assertion criteria
ATP2A3-related disorder
-
ATP2A3 p.Asp426Gly
Likely benign
No assertion criteria
ATP2A3-related disorder
-
ATP2A3 p.Asp458Asn
Benign
No assertion criteria
ATP2A3-related disorder
All ATP2A3 variants
Conflicting classifications of pathogenicity 2
- p.Arg924Trp Single submitter ⚠
- p.Pro505Leu Single submitter ⚠
Benign 24
- p.Arg491= Multiple submitters
- p.Ser877= Multiple submitters
- c.2980+691C>T Single submitter
- p.Ile332= Single submitter
- p.Pro42= Single submitter
- c.1419+10G>A No assertion criteria ATP2A3-related disorder
- c.2863-5G>A No assertion criteria ATP2A3-related disorder
- c.*14A>G No assertion criteria ATP2A3-related disorder
- c.*19A>G No assertion criteria ATP2A3-related disorder
- p.Ala424= No assertion criteria ATP2A3-related disorder
- p.Ala632= No assertion criteria ATP2A3-related disorder
- p.Arg290= No assertion criteria ATP2A3-related disorder
- p.Arg674His No assertion criteria ATP2A3-related disorder ⚠
- p.Asp458Asn No assertion criteria ATP2A3-related disorder ⚠
- p.Asp800= No assertion criteria ATP2A3-related disorder
- p.Asp887Asn No assertion criteria ATP2A3-related disorder
- p.His5= No assertion criteria ATP2A3-related disorder
- p.Leu302= No assertion criteria ATP2A3-related disorder
- p.Ser132= No assertion criteria ATP2A3-related disorder
- p.Ser917= No assertion criteria ATP2A3-related disorder
- p.Thr484= No assertion criteria ATP2A3-related disorder
- p.Thr506= No assertion criteria ATP2A3-related disorder
- p.Thr701= No assertion criteria ATP2A3-related disorder
- p.Tyr434= No assertion criteria ATP2A3-related disorder
Likely benign 32
- c.2525-6C>G Multiple submitters
- p.Ala299= Multiple submitters
- p.Arg674Cys Multiple submitters ⚠
- c.1420-5C>T Single submitter
- p.Ala27Glu Single submitter
- p.Ala569Val Single submitter ⚠
- p.Asp579= Single submitter
- p.Ile743= Single submitter
- p.Ile865Val Single submitter
- p.Pro784= Single submitter
- p.Ser915= Single submitter
- c.1095+9C>T No assertion criteria ATP2A3-related disorder
- c.1420-4G>A No assertion criteria ATP2A3-related disorder
- p.Ala223= No assertion criteria ATP2A3-related disorder
- p.Ala331= No assertion criteria ATP2A3-related disorder
- p.Ala569= No assertion criteria ATP2A3-related disorder
- p.Ala745Asp No assertion criteria ATP2A3-related disorder ⚠
- p.Asp203= No assertion criteria ATP2A3-related disorder
- p.Asp426Gly No assertion criteria ATP2A3-related disorder ⚠
- p.Glu439= No assertion criteria ATP2A3-related disorder
- p.Glu892Lys No assertion criteria ATP2A3-related disorder
- p.Ile166= No assertion criteria ATP2A3-related disorder
- p.Phe593= No assertion criteria ATP2A3-related disorder
- p.Pro308= No assertion criteria ATP2A3-related disorder
- p.Pro312= No assertion criteria ATP2A3-related disorder
- p.Pro603= No assertion criteria ATP2A3-related disorder
- p.Ser385= No assertion criteria ATP2A3-related disorder
- p.Thr457= No assertion criteria ATP2A3-related disorder
- p.Thr499= No assertion criteria ATP2A3-related disorder
- p.Thr86= No assertion criteria ATP2A3-related disorder
- p.Tyr843= No assertion criteria ATP2A3-related disorder
- p.Val916= No assertion criteria ATP2A3-related disorder
Uncertain significance 132
- p.Ala112Thr Single submitter ⚠
- p.Ala219Val Single submitter ⚠
- p.Ala327Ser Single submitter ⚠
- p.Ala32Gly Single submitter ⚠
- p.Ala372Asp Single submitter ⚠
- p.Ala3Val Single submitter ⚠
- p.Ala418Ser Single submitter ⚠
- p.Ala4Ser Single submitter ⚠
- p.Ala569Thr Single submitter ⚠
- p.Ala608Pro Single submitter ⚠
- p.Ala617Val Single submitter ⚠
- p.Ala649Thr Single submitter ⚠
- p.Ala652Pro Single submitter ⚠
- p.Ala673Thr Single submitter ⚠
- p.Ala677Thr Single submitter ⚠
- p.Ala745Thr Single submitter ⚠
- p.Ala912Ser Single submitter ⚠
- p.Arg110His Single submitter ⚠
- p.Arg131His Single submitter ⚠
- p.Arg134His Single submitter ⚠
- p.Arg141Cys Single submitter ⚠
- p.Arg143Gln Single submitter ⚠
- p.Arg143Trp Single submitter ⚠
- p.Arg164Cys Single submitter ⚠
- p.Arg324Gln Single submitter ⚠
- p.Arg324Trp Single submitter ⚠
- p.Arg325Cys Single submitter ⚠
- p.Arg328Cys Single submitter ⚠
- p.Arg33Gln Single submitter ⚠
- p.Arg464Trp Single submitter ⚠
- p.Arg467Gln Single submitter ⚠
- p.Arg480Gln Single submitter ⚠
- p.Arg529His Single submitter ⚠
- p.Arg550Gln Single submitter ⚠
- p.Arg572Lys Single submitter ⚠
- p.Arg613Cys Single submitter ⚠
- p.Arg613His Single submitter ⚠
- p.Arg637Cys Single submitter ⚠
- p.Arg63Cys Single submitter ⚠
- p.Arg686Cys Single submitter ⚠
- p.Arg686His Single submitter ⚠
- p.Arg762His Single submitter ⚠
- p.Arg822Gln Single submitter ⚠
- p.Arg825Gly Single submitter ⚠
- p.Arg965His Single submitter ⚠
- p.Asn101Asp Single submitter ⚠
- p.Asn275Thr Single submitter ⚠
- p.Asn330Lys Single submitter ⚠
- p.Asp11Glu Single submitter ⚠
- p.Asp176Asn Single submitter ⚠
- p.Asp399Asn Single submitter ⚠
- p.Asp580Asn Single submitter ⚠
- p.Cys581Ser Single submitter ⚠
- p.Cys581Tyr Single submitter ⚠
- p.Gln616Glu Single submitter ⚠
- p.Glu109Gly Single submitter ⚠
- p.Glu21Lys Single submitter ⚠
- p.Glu243Lys Single submitter ⚠
- p.Glu245Gln Single submitter ⚠
- p.Glu381Gly Single submitter ⚠
- p.Glu45Asp Single submitter ⚠
- p.Glu664Gln Single submitter ⚠
- p.Glu664Lys Single submitter ⚠
- p.Glu82Lys Single submitter ⚠
- p.Glu878Lys Single submitter ⚠
- p.Glu892Gly Single submitter ⚠
- p.Glu994Gly Single submitter ⚠
- p.Gly227Ser Single submitter ⚠
- p.Gly398Arg Single submitter ⚠
- p.Gly405Ser Single submitter ⚠
- p.Gly630Val Single submitter ⚠
- p.Gly845Ser Single submitter ⚠
- p.Gly885Ser Single submitter ⚠
- p.Gly964Arg Single submitter ⚠
- p.Ile145Val Single submitter ⚠
- p.Ile194Val Single submitter ⚠
- p.Ile816Val Single submitter ⚠
- p.Ile907Thr Single submitter ⚠
- p.Leu311Ile Single submitter ⚠
- p.Leu41Pro Single submitter ⚠
- p.Leu7Phe Single submitter ⚠
- p.Leu913Phe Single submitter ⚠
- p.Leu962Val Single submitter ⚠
- p.Met239Thr Single submitter ⚠
- p.Met452Ile Single submitter ⚠
- p.Met733Val Single submitter ⚠
- p.Met996Val Single submitter ⚠
- p.Phe57Ser Single submitter ⚠
- p.Pro124Thr Single submitter ⚠
- p.Pro26Leu Single submitter ⚠
- p.Pro282Leu Single submitter ⚠
- p.Pro312Leu Single submitter ⚠
- p.Pro391Arg Single submitter ⚠
- p.Pro500Ser Single submitter ⚠
- p.Pro536Ser Single submitter ⚠
- p.Pro602Leu Single submitter ⚠
- p.Pro824Ser Single submitter ⚠
- p.Pro881Ala Single submitter ⚠
- p.Pro881Leu Single submitter ⚠
- p.Ser170Tyr Single submitter ⚠
- p.Ser216Leu Single submitter ⚠
- p.Ser526Thr Single submitter ⚠
- p.Ser917Leu Single submitter ⚠
- p.Thr172Lys Single submitter ⚠
- p.Thr230Ser Single submitter ⚠
- p.Thr390Asn Single submitter ⚠
- p.Thr390Ile Single submitter ⚠
- p.Thr441Met Single submitter ⚠
- p.Thr654Met Single submitter ⚠
- p.Thr724Met Single submitter ⚠
- p.Tyr754Cys Single submitter ⚠
- p.Tyr986His Single submitter ⚠
- p.Val106Glu Single submitter ⚠
- p.Val106Met Single submitter ⚠
- p.Val137Met Single submitter ⚠
- p.Val185Met Single submitter ⚠
- p.Val200Met Single submitter ⚠
- p.Val224Met Single submitter ⚠
- p.Val269Met Single submitter ⚠
- p.Val271Met Single submitter ⚠
- p.Val300Met Single submitter ⚠
- p.Val339Met Single submitter ⚠
- p.Val597Ile Single submitter ⚠
- p.Val679Met Single submitter ⚠
- p.Val773Ile Single submitter ⚠
- p.Val842Gly Single submitter ⚠
- p.Val890Met Single submitter ⚠
- p.Val89Ala Single submitter ⚠
- p.Val89Met Single submitter ⚠
- p.Val916Ile Single submitter ⚠
- p.Val950Met Single submitter ⚠
- p.Val959Met Single submitter ⚠