KDM2A — 109 ClinVar variants
All ClinVar germline KDM2A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 82 flagged for review →
9 Pathogenic · 11 Likely pathogenic · 2 Benign · 1 Likely benign · 86 Uncertain significance
Full KDM2A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 82
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 1
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
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KDM2A p.His811Asn
Likely pathogenic
Single submitter
KDM2A-related neurodevelopmental disorder
Predictors lean, ClinVar uncertain 62
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- KDM2A p.Ala940Val Uncertain significance Single submitter
- KDM2A p.Arg261Trp Uncertain significance Single submitter
- KDM2A p.Arg347His Uncertain significance Single submitter
- KDM2A p.Arg380Gly Uncertain significance Single submitter
- KDM2A p.Arg412Gln Uncertain significance Single submitter
- KDM2A p.Arg753His Uncertain significance Single submitter
- KDM2A p.Arg834Cys Uncertain significance Single submitter
- KDM2A p.Arg843Gln Uncertain significance Single submitter
- KDM2A p.Arg847Cys Uncertain significance Single submitter
- KDM2A p.Arg881Gln Uncertain significance Single submitter
- KDM2A p.Arg903Cys Uncertain significance Single submitter
- KDM2A p.Arg915Pro Uncertain significance Single submitter
- KDM2A p.Asn1147Ser Uncertain significance Single submitter
- KDM2A p.Asn322Ser Uncertain significance Single submitter
- KDM2A p.Asn974Ser Uncertain significance Single submitter
- KDM2A p.Asp374Asn Uncertain significance Single submitter
- KDM2A p.Asp424Gly Uncertain significance Single submitter
- KDM2A p.Asp428Glu Uncertain significance Single submitter
- KDM2A p.Asp657Tyr Uncertain significance Single submitter
- KDM2A p.Asp867Tyr Uncertain significance Single submitter
- KDM2A p.Cys642Ser Uncertain significance Single submitter
- KDM2A p.Cys708Ser Uncertain significance Single submitter
- KDM2A p.Gln655Glu Uncertain significance Single submitter
- KDM2A p.Gln766His Uncertain significance Single submitter
- KDM2A p.Glu671Val Uncertain significance Single submitter
- KDM2A p.Glu694Lys Uncertain significance Single submitter
- KDM2A p.Glu695Gln Uncertain significance Single submitter
- KDM2A p.Glu777Gln Uncertain significance Single submitter
- KDM2A p.Glu857Asp Uncertain significance Single submitter
- KDM2A p.His1076Tyr Uncertain significance Single submitter
- KDM2A p.His727Arg Uncertain significance Single submitter
- KDM2A p.His749Tyr Uncertain significance Single submitter
- KDM2A p.Ile119Val Uncertain significance Single submitter
- KDM2A p.Ile67Val Uncertain significance Single submitter
- KDM2A p.Leu508Phe Uncertain significance Single submitter
- KDM2A p.Leu829Val Uncertain significance Single submitter
- KDM2A p.Leu984Val Uncertain significance Single submitter
- KDM2A p.Lys1106Gln Uncertain significance Single submitter
- KDM2A p.Lys686Arg Uncertain significance Single submitter
- KDM2A p.Lys758Gln Uncertain significance Single submitter
-
KDM2A p.Lys776Arg
Uncertain significance
Single submitter
KDM2A-related neurodevelopmental disorder
- KDM2A p.Met156Val Uncertain significance Single submitter
- KDM2A p.Met735Val Uncertain significance Single submitter
-
KDM2A p.Phe524Cys
Uncertain significance
Single submitter
KDM2A-related neurodevelopmental disorder
- KDM2A p.Pro1025Ala Uncertain significance Single submitter
- KDM2A p.Pro1026Leu Uncertain significance Single submitter
- KDM2A p.Pro1030Leu Uncertain significance Single submitter
- KDM2A p.Pro504Ala Uncertain significance Single submitter
- KDM2A p.Pro559Leu Uncertain significance Single submitter
- KDM2A p.Pro704Ala Uncertain significance Single submitter
- KDM2A p.Ser360Asn Uncertain significance Single submitter
- KDM2A p.Ser416Ile Uncertain significance Single submitter
- KDM2A p.Ser603Cys Uncertain significance Single submitter
- KDM2A p.Ser707Gly Uncertain significance Single submitter
- KDM2A p.Thr542Ala Uncertain significance Single submitter
- KDM2A p.Thr720Ala Uncertain significance Single submitter
- KDM2A p.Thr737Ser Uncertain significance Single submitter
- KDM2A p.Thr813Ile Uncertain significance Single submitter
- KDM2A p.Val1121Ile Uncertain significance Single submitter
- KDM2A p.Val64Ile Uncertain significance Single submitter
- KDM2A p.Val730Gly Uncertain significance Single submitter
- KDM2A p.Val973Ile Uncertain significance Single submitter
Predictors split 19
The independent predictors disagree with each other — read with care.
- KDM2A p.Arg1117Cys Uncertain significance Single submitter
- KDM2A p.Arg175Ser Uncertain significance Single submitter
- KDM2A p.Arg519Ser Uncertain significance Single submitter
- KDM2A p.Asp164Tyr Uncertain significance Single submitter
- KDM2A p.Cys925Tyr Uncertain significance Single submitter
- KDM2A p.Gln761His Uncertain significance Single submitter
- KDM2A p.Gln944His Uncertain significance Single submitter
- KDM2A p.Glu647Asp Uncertain significance Single submitter
- KDM2A p.Glu858Lys Uncertain significance Single submitter
- KDM2A p.Gly658Arg Uncertain significance Single submitter
- KDM2A p.Leu946Phe Uncertain significance Single submitter
- KDM2A p.Lys1037Met Uncertain significance Single submitter
-
KDM2A p.Lys776Asn
Uncertain significance
Single submitter
KDM2A-related neurodevelopmental disorder
- KDM2A p.Lys918Gln Uncertain significance Single submitter
- KDM2A p.Met899Ile Uncertain significance Single submitter
- KDM2A p.Ser617Leu Uncertain significance Single submitter
- KDM2A p.Ser993Phe Uncertain significance Single submitter
- KDM2A p.Thr1111Ile Uncertain significance Single submitter
- KDM2A p.Tyr330His Uncertain significance Single submitter
All KDM2A variants
Pathogenic 9
- p.Arg20Ter Single submitter KDM2A-related neurodevelopmental disorder
- p.Arg325fs Single submitter
- p.Arg383Ter Single submitter
- p.Asp889fs Single submitter KDM2A-related neurodevelopmental disorder
- p.Cys642fs Single submitter
- p.Cys938Ter Single submitter KDM2A-related neurodevelopmental disorder
- p.Gly432fs Single submitter cataract 4 multiple types
- p.Ile560fs Single submitter KDM2A-related neurodevelopmental disorder
- p.Tyr193Ter Single submitter KDM2A-related neurodevelopmental disorder
Likely pathogenic 11
- p.His284Tyr Multiple submitters KDM2A-related neurodevelopmental disorder
- p.Met591Thr Multiple submitters KDM2A-related neurodevelopmental disorder
- p.Arg319Gln Single submitter KDM2A-related neurodevelopmental disorder
- p.Arg568Gln Single submitter KDM2A-related neurodevelopmental disorder
- p.Arg568Gly Single submitter neurodevelopmental disorder
- p.Arg599Pro Single submitter KDM2A-related neurodevelopmental disorder
- p.His811Asn Single submitter KDM2A-related neurodevelopmental disorder ⚠
- p.Lys593del Single submitter
- p.Pro235Leu Single submitter KDM2A-related neurodevelopmental disorder
- p.Thr802fs Single submitter KDM2A-related neurodevelopmental disorder
- p.Tyr141Cys Single submitter KDM2A-related neurodevelopmental disorder
Benign 2
- p.Cys1151= Multiple submitters
- p.Thr351= Multiple submitters
Likely benign 1
- p.Gly432= Single submitter
Uncertain significance 86
- c.43-2A>G Single submitter
- p.Ala940Val Single submitter ⚠
- p.Arg1117Cys Single submitter ⚠
- p.Arg175Ser Single submitter ⚠
- p.Arg205Ter Single submitter
- p.Arg261Trp Single submitter ⚠
- p.Arg347His Single submitter ⚠
- p.Arg380Gly Single submitter ⚠
- p.Arg412Gln Single submitter ⚠
- p.Arg519Ser Single submitter ⚠
- p.Arg753His Single submitter ⚠
- p.Arg834Cys Single submitter ⚠
- p.Arg843Gln Single submitter ⚠
- p.Arg847Cys Single submitter ⚠
- p.Arg881Gln Single submitter ⚠
- p.Arg903Cys Single submitter ⚠
- p.Arg915Pro Single submitter ⚠
- p.Asn1147Ser Single submitter ⚠
- p.Asn322Ser Single submitter ⚠
- p.Asn974Ser Single submitter ⚠
- p.Asp164Tyr Single submitter ⚠
- p.Asp374Asn Single submitter ⚠
- p.Asp424Gly Single submitter ⚠
- p.Asp428Glu Single submitter ⚠
- p.Asp657Tyr Single submitter ⚠
- p.Asp867Tyr Single submitter ⚠
- p.Cys642Ser Single submitter ⚠
- p.Cys708Ser Single submitter ⚠
- p.Cys925Tyr Single submitter ⚠
- p.Gln655Glu Single submitter ⚠
- p.Gln761His Single submitter ⚠
- p.Gln766His Single submitter ⚠
- p.Gln944His Single submitter ⚠
- p.Glu647Asp Single submitter ⚠
- p.Glu671Val Single submitter ⚠
- p.Glu694Lys Single submitter ⚠
- p.Glu695Gln Single submitter ⚠
- p.Glu777Gln Single submitter ⚠
- p.Glu857Asp Single submitter ⚠
- p.Glu858Lys Single submitter ⚠
- p.Gly658Arg Single submitter ⚠
- p.His1076Tyr Single submitter ⚠
- p.His727Arg Single submitter ⚠
- p.His749Tyr Single submitter ⚠
- p.Ile119Val Single submitter ⚠
- p.Ile67Val Single submitter ⚠
- p.Leu508Phe Single submitter ⚠
- p.Leu829Val Single submitter ⚠
- p.Leu946Phe Single submitter ⚠
- p.Leu984Val Single submitter ⚠
- p.Lys1037Met Single submitter ⚠
- p.Lys1106Gln Single submitter ⚠
- p.Lys117fs Single submitter
- p.Lys686Arg Single submitter ⚠
- p.Lys758Gln Single submitter ⚠
- p.Lys776Arg Single submitter KDM2A-related neurodevelopmental disorder ⚠
- p.Lys776Asn Single submitter KDM2A-related neurodevelopmental disorder ⚠
- p.Lys918Gln Single submitter ⚠
- p.Met156Val Single submitter ⚠
- p.Met735Val Single submitter ⚠
- p.Met899Ile Single submitter ⚠
- p.Phe524Cys Single submitter KDM2A-related neurodevelopmental disorder ⚠
- p.Pro1025Ala Single submitter ⚠
- p.Pro1026Leu Single submitter ⚠
- p.Pro1030Leu Single submitter ⚠
- p.Pro504Ala Single submitter ⚠
- p.Pro559Leu Single submitter ⚠
- p.Pro704Ala Single submitter ⚠
- p.Ser360Asn Single submitter ⚠
- p.Ser416Ile Single submitter ⚠
- p.Ser427del Single submitter
- p.Ser603Cys Single submitter ⚠
- p.Ser617Leu Single submitter ⚠
- p.Ser707Gly Single submitter ⚠
- p.Ser993Phe Single submitter ⚠
- p.Thr1111Ile Single submitter ⚠
- p.Thr542Ala Single submitter ⚠
- p.Thr720Ala Single submitter ⚠
- p.Thr737Ser Single submitter ⚠
- p.Thr813Ile Single submitter ⚠
- p.Tyr244Ter Single submitter KDM2A-related disorder
- p.Tyr330His Single submitter ⚠
- p.Val1121Ile Single submitter ⚠
- p.Val64Ile Single submitter ⚠
- p.Val730Gly Single submitter ⚠
- p.Val973Ile Single submitter ⚠