KDM3A — 177 ClinVar variants
All ClinVar germline KDM3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 135 flagged for review →
15 Benign · 1 Benign/Likely benign · 19 Likely benign · 142 Uncertain significance
Full KDM3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 135
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 113
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- KDM3A p.Ala307Thr Uncertain significance Single submitter
- KDM3A p.Ala322Thr Uncertain significance Single submitter
- KDM3A p.Ala409Val Uncertain significance Single submitter
- KDM3A p.Ala422Ser Uncertain significance Single submitter
- KDM3A p.Ala457Thr Uncertain significance Single submitter
- KDM3A p.Ala518Thr Uncertain significance Single submitter
- KDM3A p.Ala518Val Uncertain significance Single submitter
- KDM3A p.Ala743Val Uncertain significance Single submitter
- KDM3A p.Ala816Thr Uncertain significance Single submitter
- KDM3A p.Arg107Gln Uncertain significance Single submitter
- KDM3A p.Arg1112Gln Uncertain significance Single submitter
- KDM3A p.Arg1216Gln Uncertain significance Single submitter
- KDM3A p.Arg1281Gln Uncertain significance Single submitter
- KDM3A p.Arg37Cys Uncertain significance Single submitter
- KDM3A p.Arg569His Uncertain significance Single submitter
- KDM3A p.Asn1068Ile Uncertain significance Single submitter
- KDM3A p.Asn1253Lys Uncertain significance Single submitter
- KDM3A p.Asn451Asp Uncertain significance Single submitter
- KDM3A p.Asn465Lys Uncertain significance Single submitter
- KDM3A p.Asn483Tyr Uncertain significance Single submitter
- KDM3A p.Asn501Ile Uncertain significance Single submitter
- KDM3A p.Asn502Ser Uncertain significance Single submitter
- KDM3A p.Asn579Ser Uncertain significance Single submitter
- KDM3A p.Asn593Ser Uncertain significance Single submitter
- KDM3A p.Asn879Ser Uncertain significance Single submitter
- KDM3A p.Asp362Gly Uncertain significance Single submitter
- KDM3A p.Asp462Glu Uncertain significance Single submitter
- KDM3A p.Asp940Asn Uncertain significance Single submitter
- KDM3A p.Cys225Arg Uncertain significance Single submitter
- KDM3A p.Cys337Arg Uncertain significance Single submitter
- KDM3A p.Cys349Phe Uncertain significance Single submitter
- KDM3A p.Cys814Phe Uncertain significance Single submitter
- KDM3A p.Gln110Arg Uncertain significance Single submitter
- KDM3A p.Gln340Pro Uncertain significance Single submitter
- KDM3A p.Glu1165Lys Uncertain significance Single submitter
- KDM3A p.Glu1187Ala Uncertain significance Single submitter
- KDM3A p.Glu454Lys Uncertain significance Single submitter
- KDM3A p.Glu70Gln Uncertain significance Single submitter
- KDM3A p.Glu768Ala Uncertain significance Single submitter
- KDM3A p.Gly1021Ala Uncertain significance Single submitter
- KDM3A p.Gly1105Ala Uncertain significance Single submitter
- KDM3A p.Gly1319Arg Uncertain significance Single submitter
- KDM3A p.Gly186Val Uncertain significance Single submitter
- KDM3A p.Gly367Arg Uncertain significance Single submitter
- KDM3A p.Gly376Arg Uncertain significance Single submitter
- KDM3A p.Gly412Ala Uncertain significance Single submitter
- KDM3A p.Gly458Asp Uncertain significance Single submitter
- KDM3A p.Gly830Arg Uncertain significance Single submitter
- KDM3A p.Gly929Glu Uncertain significance Single submitter
- KDM3A p.His439Arg Uncertain significance Single submitter
- KDM3A p.His628Arg Uncertain significance Single submitter
- KDM3A p.His867Pro Uncertain significance Single submitter
- KDM3A p.Ile114Val Uncertain significance Single submitter
- KDM3A p.Ile1160Leu Uncertain significance Single submitter
- KDM3A p.Ile1164Val Uncertain significance Single submitter
- KDM3A p.Ile128Val Uncertain significance Single submitter
- KDM3A p.Ile165Leu Uncertain significance Single submitter
- KDM3A p.Ile257Met Uncertain significance Single submitter
- KDM3A p.Ile48Val Uncertain significance Single submitter
- KDM3A p.Ile625Val Uncertain significance Single submitter
- KDM3A p.Ile714Lys Uncertain significance Single submitter
- KDM3A p.Leu329Val Uncertain significance Single submitter
- KDM3A p.Leu369Val Uncertain significance Single submitter
- KDM3A p.Leu584Trp Uncertain significance Single submitter
- KDM3A p.Leu5Val Uncertain significance Single submitter
- KDM3A p.Leu707Val Uncertain significance Single submitter
- KDM3A p.Leu782Val Uncertain significance Single submitter
- KDM3A p.Leu866Phe Uncertain significance Single submitter
- KDM3A p.Lys1137Arg Uncertain significance Single submitter
- KDM3A p.Lys117Arg Uncertain significance Single submitter
- KDM3A p.Lys1191Arg Uncertain significance Single submitter
- KDM3A p.Lys312Glu Uncertain significance Single submitter
- KDM3A p.Lys332Arg Uncertain significance Single submitter
- KDM3A p.Lys415Glu Uncertain significance Single submitter
- KDM3A p.Lys905Thr Uncertain significance Single submitter
- KDM3A p.Lys984Gln Uncertain significance Single submitter
- KDM3A p.Met286Thr Uncertain significance Single submitter
- KDM3A p.Met640Val Uncertain significance Single submitter
- KDM3A p.Met843Val Uncertain significance Single submitter
- KDM3A p.Met977Leu Uncertain significance Single submitter
- KDM3A p.Phe1318Ile Uncertain significance Single submitter
- KDM3A p.Phe530Val Uncertain significance Single submitter
- KDM3A p.Phe578Tyr Uncertain significance Single submitter
- KDM3A p.Pro102Ser Uncertain significance Single submitter
- KDM3A p.Pro10Leu Uncertain significance Single submitter
- KDM3A p.Pro293Arg Uncertain significance Single submitter
- KDM3A p.Pro565Thr Uncertain significance Single submitter
- KDM3A p.Pro780Leu Uncertain significance Single submitter
- KDM3A p.Pro795Gln Uncertain significance Single submitter
- KDM3A p.Pro812Ala Uncertain significance Single submitter
- KDM3A p.Pro855Ala Uncertain significance Single submitter
- KDM3A p.Pro927Thr Uncertain significance Single submitter
- KDM3A p.Ser1060Phe Uncertain significance Single submitter
- KDM3A p.Ser1314Asn Uncertain significance Single submitter
- KDM3A p.Ser26Gly Uncertain significance Single submitter
- KDM3A p.Ser325Phe Uncertain significance Single submitter
- KDM3A p.Ser32Gly Uncertain significance Single submitter
- KDM3A p.Ser553Ile Uncertain significance Single submitter
- KDM3A p.Ser705Phe Uncertain significance Single submitter
- KDM3A p.Ser892Cys Uncertain significance Single submitter
- KDM3A p.Thr1011Asn Uncertain significance Single submitter
- KDM3A p.Thr295Ala Uncertain significance Single submitter
- KDM3A p.Thr295Arg Uncertain significance Single submitter
- KDM3A p.Thr308Ala Uncertain significance Single submitter
- KDM3A p.Thr411Ile Uncertain significance Single submitter
- KDM3A p.Thr642Ala Uncertain significance Single submitter
- KDM3A p.Thr828Ala Uncertain significance Single submitter
- KDM3A p.Val11Ile Uncertain significance Single submitter
- KDM3A p.Val11Leu Uncertain significance Single submitter
- KDM3A p.Val175Leu Uncertain significance Single submitter
- KDM3A p.Val531Ile Uncertain significance Single submitter
- KDM3A p.Val540Met Uncertain significance Single submitter
- KDM3A p.Val741Leu Uncertain significance Single submitter
Predictors split 22
The independent predictors disagree with each other — read with care.
- KDM3A p.Ala97Val Uncertain significance Single submitter
- KDM3A p.Arg1112Trp Uncertain significance Single submitter
- KDM3A p.Arg262Leu Uncertain significance Single submitter
- KDM3A p.Arg550His Uncertain significance Single submitter
- KDM3A p.Arg99Gln Uncertain significance Single submitter
- KDM3A p.Asp1152Gly Uncertain significance Single submitter
- KDM3A p.Glu1052Asp Uncertain significance Single submitter
- KDM3A p.Leu147Trp Uncertain significance Single submitter
- KDM3A p.Leu590Phe Uncertain significance Single submitter
- KDM3A p.Leu888Pro Uncertain significance Single submitter
- KDM3A p.Leu914Phe Uncertain significance Single submitter
- KDM3A p.Lys619Gln Uncertain significance Single submitter
- KDM3A p.Met1057Thr Uncertain significance Single submitter
- KDM3A p.Pro1201Gln Uncertain significance Single submitter
- KDM3A p.Ser1155Phe Uncertain significance Single submitter
- KDM3A p.Ser564Pro Uncertain significance Single submitter
- KDM3A p.Thr115Met Likely benign Single submitter
- KDM3A p.Thr1182Met Uncertain significance Single submitter
- KDM3A p.Tyr1255His Uncertain significance Single submitter
- KDM3A p.Val685Ala Uncertain significance Single submitter
-
KDM3A p.His1204Tyr
Uncertain significance
No assertion criteria
KDM3A-related disorder
-
KDM3A p.Leu520His
Benign
No assertion criteria
KDM3A-related disorder
All KDM3A variants
Benign 15
- c.2512+19T>C Multiple submitters
- p.Leu937= Multiple submitters
- c.557-5_557-4del No assertion criteria KDM3A-related disorder
- c.557-6_557-4dup No assertion criteria KDM3A-related disorder
- p.Ala1261= No assertion criteria KDM3A-related disorder
- p.Ala639= No assertion criteria KDM3A-related disorder
- p.Ala825= No assertion criteria KDM3A-related disorder
- p.Glu1037= No assertion criteria KDM3A-related disorder
- p.Glu1187= No assertion criteria KDM3A-related disorder
- p.Gly1319= No assertion criteria KDM3A-related disorder
- p.Leu520= No assertion criteria KDM3A-related disorder
- p.Leu520His No assertion criteria KDM3A-related disorder ⚠
- p.Pro780= No assertion criteria KDM3A-related disorder
- p.Ser447Pro No assertion criteria KDM3A-related disorder
- p.Val1131Ile No assertion criteria KDM3A-related disorder
Benign/Likely benign 1
- p.Leu1283= Multiple submitters
Likely benign 19
- p.Val63= Multiple submitters
- c.453+5A>G Single submitter
- p.Ala452Thr Single submitter
- p.Arg15Lys Single submitter
- p.Arg692Lys Single submitter
- p.Asn597Ser Single submitter
- p.Cys417Phe Single submitter
- p.Gly830= Single submitter
- p.Ile1069= Single submitter
- p.Met286Val Single submitter
- p.Ser21= Single submitter
- p.Thr115Met Single submitter ⚠
- c.754+9T>C No assertion criteria KDM3A-related disorder
- p.Ala307= No assertion criteria KDM3A-related disorder
- p.Asp152= No assertion criteria KDM3A-related disorder
- p.His92Arg No assertion criteria KDM3A-related disorder
- p.Leu413= No assertion criteria KDM3A-related disorder
- p.Lys263= No assertion criteria KDM3A-related disorder
- p.Val566= No assertion criteria KDM3A-related disorder
Uncertain significance 142
- c.1940-2A>G Single submitter
- c.681+1dup Single submitter
- p.Ala307Thr Single submitter ⚠
- p.Ala322Thr Single submitter ⚠
- p.Ala409Val Single submitter ⚠
- p.Ala422Ser Single submitter ⚠
- p.Ala457Thr Single submitter ⚠
- p.Ala518Thr Single submitter ⚠
- p.Ala518Val Single submitter ⚠
- p.Ala743Val Single submitter ⚠
- p.Ala816Thr Single submitter ⚠
- p.Ala97Val Single submitter ⚠
- p.Arg107Gln Single submitter ⚠
- p.Arg1112Gln Single submitter ⚠
- p.Arg1112Trp Single submitter ⚠
- p.Arg1216Gln Single submitter ⚠
- p.Arg1281Gln Single submitter ⚠
- p.Arg262Leu Single submitter ⚠
- p.Arg37Cys Single submitter ⚠
- p.Arg547Ter Single submitter
- p.Arg550His Single submitter ⚠
- p.Arg569His Single submitter ⚠
- p.Arg99Gln Single submitter ⚠
- p.Asn1068Ile Single submitter ⚠
- p.Asn1253Lys Single submitter ⚠
- p.Asn451Asp Single submitter ⚠
- p.Asn465Lys Single submitter ⚠
- p.Asn483Tyr Single submitter ⚠
- p.Asn501Ile Single submitter ⚠
- p.Asn502Ser Single submitter ⚠
- p.Asn579Ser Single submitter ⚠
- p.Asn593Ser Single submitter ⚠
- p.Asn879Ser Single submitter ⚠
- p.Asp1152Gly Single submitter ⚠
- p.Asp362Gly Single submitter ⚠
- p.Asp462Glu Single submitter ⚠
- p.Asp940Asn Single submitter ⚠
- p.Cys225Arg Single submitter ⚠
- p.Cys337Arg Single submitter ⚠
- p.Cys349Phe Single submitter ⚠
- p.Cys814Phe Single submitter ⚠
- p.Gln110Arg Single submitter ⚠
- p.Gln340Pro Single submitter ⚠
- p.Glu1052Asp Single submitter ⚠
- p.Glu1165Lys Single submitter ⚠
- p.Glu1187Ala Single submitter ⚠
- p.Glu454Lys Single submitter ⚠
- p.Glu70Gln Single submitter ⚠
- p.Glu768Ala Single submitter ⚠
- p.Gly1021Ala Single submitter ⚠
- p.Gly1105Ala Single submitter ⚠
- p.Gly1319Arg Single submitter ⚠
- p.Gly186Val Single submitter ⚠
- p.Gly367Arg Single submitter ⚠
- p.Gly376Arg Single submitter ⚠
- p.Gly412Ala Single submitter ⚠
- p.Gly458Asp Single submitter ⚠
- p.Gly830Arg Single submitter ⚠
- p.Gly929Glu Single submitter ⚠
- p.His439Arg Single submitter ⚠
- p.His628Arg Single submitter ⚠
- p.His867Pro Single submitter ⚠
- p.Ile114Val Single submitter ⚠
- p.Ile1160Leu Single submitter ⚠
- p.Ile1164Val Single submitter ⚠
- p.Ile128Val Single submitter ⚠
- p.Ile165Leu Single submitter ⚠
- p.Ile257Met Single submitter ⚠
- p.Ile48Val Single submitter ⚠
- p.Ile625Val Single submitter ⚠
- p.Ile714Lys Single submitter ⚠
- p.Leu1147Arg Single submitter
- p.Leu147Trp Single submitter ⚠
- p.Leu329Val Single submitter ⚠
- p.Leu369Val Single submitter ⚠
- p.Leu584Trp Single submitter ⚠
- p.Leu590Phe Single submitter ⚠
- p.Leu5Val Single submitter ⚠
- p.Leu707Val Single submitter ⚠
- p.Leu782Val Single submitter ⚠
- p.Leu866Phe Single submitter ⚠
- p.Leu888Pro Single submitter ⚠
- p.Leu914Phe Single submitter ⚠
- p.Lys1137Arg Single submitter ⚠
- p.Lys117Arg Single submitter ⚠
- p.Lys1191Arg Single submitter ⚠
- p.Lys312Glu Single submitter ⚠
- p.Lys332Arg Single submitter ⚠
- p.Lys415Glu Single submitter ⚠
- p.Lys619Gln Single submitter ⚠
- p.Lys905Thr Single submitter ⚠
- p.Lys984Gln Single submitter ⚠
- p.Met1057Thr Single submitter ⚠
- p.Met286Thr Single submitter ⚠
- p.Met640Val Single submitter ⚠
- p.Met843Val Single submitter ⚠
- p.Met977Leu Single submitter ⚠
- p.Phe1318Ile Single submitter ⚠
- p.Phe530Val Single submitter ⚠
- p.Phe578Tyr Single submitter ⚠
- p.Pro102Ser Single submitter ⚠
- p.Pro10Leu Single submitter ⚠
- p.Pro1201Gln Single submitter ⚠
- p.Pro293Arg Single submitter ⚠
- p.Pro565Thr Single submitter ⚠
- p.Pro780Leu Single submitter ⚠
- p.Pro795Gln Single submitter ⚠
- p.Pro812Ala Single submitter ⚠
- p.Pro855Ala Single submitter ⚠
- p.Pro927Thr Single submitter ⚠
- p.Ser1060Phe Single submitter ⚠
- p.Ser1155Phe Single submitter ⚠
- p.Ser1314Asn Single submitter ⚠
- p.Ser203Phe Single submitter
- p.Ser26Gly Single submitter ⚠
- p.Ser325Phe Single submitter ⚠
- p.Ser32Gly Single submitter ⚠
- p.Ser341fs Single submitter
- p.Ser553Ile Single submitter ⚠
- p.Ser564Pro Single submitter ⚠
- p.Ser705Phe Single submitter ⚠
- p.Ser892Cys Single submitter ⚠
- p.Thr1011Asn Single submitter ⚠
- p.Thr1182Met Single submitter ⚠
- p.Thr295Ala Single submitter ⚠
- p.Thr295Arg Single submitter ⚠
- p.Thr308Ala Single submitter ⚠
- p.Thr411Ile Single submitter ⚠
- p.Thr642Ala Single submitter ⚠
- p.Thr828Ala Single submitter ⚠
- p.Trp823Ter Single submitter
- p.Tyr1255His Single submitter ⚠
- p.Val1092Ile Single submitter
- p.Val11Ile Single submitter ⚠
- p.Val11Leu Single submitter ⚠
- p.Val175Leu Single submitter ⚠
- p.Val531Ile Single submitter ⚠
- p.Val540Met Single submitter ⚠
- p.Val685Ala Single submitter ⚠
- p.Val741Leu Single submitter ⚠
- c.2685+6TGTT[2] No assertion criteria prostate cancer
- p.His1204Tyr No assertion criteria KDM3A-related disorder ⚠