KDM5A — 263 ClinVar variants

All ClinVar germline KDM5A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 197 flagged for review →

5 Pathogenic · 6 Likely pathogenic · 1 Conflicting · 11 Benign · 3 Benign/Likely benign · 31 Likely benign · 206 Uncertain significance

Full KDM5A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 197

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 1

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

KDM5A p.Pro328Leu Conflicting Single submitter

Predictors lean, ClinVar uncertain 128

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

Predictors split 68

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

All KDM5A variants

Pathogenic 5

p.Gln832Ter Single submitter El Hayek-Chahrour neurodevelopmental disorder
p.Tyr9fs Single submitter
c.2541+1G>T No assertion criteria El Hayek-Chahrour neurodevelopmental disorder
c.672+1488_1149+711del No assertion criteria El Hayek-Chahrour neurodevelopmental disorder
p.Phe477Val No assertion criteria El Hayek-Chahrour neurodevelopmental disorder

Likely pathogenic 6

c.4074+1G>A Multiple submitters El Hayek-Chahrour neurodevelopmental disorder
c.166-6_169del Single submitter El Hayek-Chahrour neurodevelopmental disorder
p.Arg1428Leu Single submitter intellectual disability ⚠
p.Arg603Ter Single submitter
p.Met1Leu Single submitter intellectual disability
p.Pro17fs Single submitter El Hayek-Chahrour neurodevelopmental disorder

Conflicting classifications of pathogenicity 1

p.Pro328Leu Single submitter ⚠

Benign 11

c.2150+7A>G Multiple submitters
p.Asp1104Gly Multiple submitters
p.Glu1446Gln Multiple submitters
p.Glu1558Val Multiple submitters ⚠
p.Met1336Val Multiple submitters
p.Met865Thr Multiple submitters
p.Pro1474Thr Multiple submitters
p.Val341= Multiple submitters
p.Val382= Multiple submitters
p.Ser454= Single submitter
p.His808Leu No assertion criteria KDM5A-related disorder

Benign/Likely benign 3

p.Ala633Thr Multiple submitters
p.Cys1180= Multiple submitters
p.Pro967= Multiple submitters

Likely benign 31

c.1653+8T>G Single submitter
c.2151-14_2151-5dup Single submitter
c.2151-15_2151-5dup Single submitter
c.2151-16_2151-5dup Single submitter
c.2151-20_2151-5del Single submitter
c.2151-22_2151-5dup Single submitter
c.2151-4G>T Single submitter
c.2151-5_2151-4insTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTT Single submitter
c.2151-7_2151-5del Single submitter
c.2151-7_2151-5dup Single submitter
c.243+4del Single submitter
p.Ala1006Thr Single submitter
p.Ala1052= Single submitter
p.Ala510= Single submitter
p.Ala621= Single submitter
p.Arg1002= Single submitter
p.Asn1372= Single submitter
p.Asn379Ser Single submitter
p.Gln946= Single submitter
p.Leu616= Single submitter
p.Lys1235= Single submitter
p.Met1683Val Single submitter
p.Pro469= Single submitter
p.Pro507= Single submitter
p.Pro523= Single submitter
p.Ser1277= Single submitter
p.Ser1438= Single submitter
p.Val797= Single submitter
c.2151-17_2151-5dup No assertion criteria KDM5A-related disorder
c.4455+6G>T No assertion criteria KDM5A-related disorder
p.Leu33= No assertion criteria KDM5A-related disorder

Uncertain significance 206

p.Ala1260Val Multiple submitters ⚠
p.Ala736Thr Multiple submitters ⚠
p.Gly630Glu Multiple submitters ⚠
p.Ile1011Thr Multiple submitters El Hayek-Chahrour neurodevelopmental disorder ⚠
p.Ser479Cys Multiple submitters ⚠
p.Ser572Cys Multiple submitters ⚠
c.244-2A>C Single submitter
c.4234+7C>A Single submitter
p.1098EK[2] Single submitter
p.Ala1018_Tyr1019del Single submitter
p.Ala1028Gly Single submitter ⚠
p.Ala1050Gly Single submitter ⚠
p.Ala1146Thr Single submitter ⚠
p.Ala11Val Single submitter ⚠
p.Ala1287Val Single submitter ⚠
p.Ala1298Ser Single submitter ⚠
p.Ala1298Val Single submitter ⚠
p.Ala1611Thr Single submitter ⚠
p.Ala1659Thr Single submitter ⚠
p.Ala589Ser Single submitter ⚠
p.Ala752Gly Single submitter ⚠
p.Ala770Ser Single submitter ⚠
p.Ala863Thr Single submitter ⚠
p.Arg1054Ser Single submitter ⚠
p.Arg1077Gln Single submitter ⚠
p.Arg1077Trp Single submitter ⚠
p.Arg1089Trp Single submitter ⚠
p.Arg112fs Single submitter
p.Arg1133Gln Single submitter ⚠
p.Arg1239Gln Single submitter ⚠
p.Arg1259Thr Single submitter ⚠
p.Arg1261Gln Single submitter ⚠
p.Arg1282Cys Single submitter ⚠
p.Arg1282His Single submitter KDM5A-related Neurodevelopmental disorder with autism ⚠
p.Arg1323Trp Single submitter ⚠
p.Arg1333Gln Single submitter ⚠
p.Arg1421Trp Single submitter ⚠
p.Arg145His Single submitter ⚠
p.Arg1508Gln Single submitter ⚠
p.Arg264Gln Single submitter ⚠
p.Arg271Ser Single submitter ⚠
p.Arg301Gly Single submitter ⚠
p.Arg359Gln Single submitter ⚠
p.Arg604Cys Single submitter ⚠
p.Arg745His Single submitter ⚠
p.Arg745Pro Single submitter KDM5A-related disorder ⚠
p.Arg76His Single submitter ⚠
p.Arg85Gly Single submitter ⚠
p.Arg87Thr Single submitter ⚠
p.Arg893Gln Single submitter ⚠
p.Arg908Thr Single submitter ⚠
p.Arg968fs Single submitter
p.Asn1372Ser Single submitter ⚠
p.Asn1614Asp Single submitter ⚠
p.Asn778Thr Single submitter ⚠
p.Asn983Ser Single submitter ⚠
p.Asp1258Gly Single submitter ⚠
p.Asp1267Gly Single submitter ⚠
p.Asp1337Glu Single submitter ⚠
p.Asp1340Glu Single submitter ⚠
p.Asp1376Gly Single submitter ⚠
p.Asp1486Glu Single submitter ⚠
p.Asp1621Gly Single submitter ⚠
p.Asp1685His Single submitter ⚠
p.Asp260Gly Single submitter ⚠
p.Asp31Gly Single submitter ⚠
p.Asp786Val Single submitter ⚠
p.Asp851His Single submitter ⚠
p.Asp852Ala Single submitter ⚠
p.Asp852Asn Single submitter ⚠
p.Cys1619Tyr Single submitter ⚠
p.Gln1197Pro Single submitter ⚠
p.Gln1286Leu Single submitter ⚠
p.Gln1444Glu Single submitter ⚠
p.Gln182Arg Single submitter ⚠
p.Gln224Glu Single submitter ⚠
p.Gln240His Single submitter ⚠
p.Gln576Ter Single submitter KDM5A-associated neurodevelopmental syndrome
p.Gln806Arg Single submitter ⚠
p.Glu1021Gly Single submitter ⚠
p.Glu1108Asp Single submitter ⚠
p.Glu1108Gly Single submitter ⚠
p.Glu1268Val Single submitter ⚠
p.Glu1342Gly Single submitter ⚠
p.Glu1519Asp Single submitter ⚠
p.Glu195Lys Single submitter ⚠
p.Glu28Gly Single submitter ⚠
p.Glu614Lys Single submitter KDM5A-related disorder ⚠
p.Glu64Asp Single submitter ⚠
p.Glu825Val Single submitter ⚠
p.Glu858Asp Single submitter ⚠
p.Glu980fs Single submitter
p.Gly1030Arg Single submitter ⚠
p.Gly1086Ser Single submitter ⚠
p.Gly1086Val Single submitter ⚠
p.Gly1116Glu Single submitter ⚠
p.Gly1354Asp Single submitter ⚠
p.Gly1520Glu Single submitter ⚠
p.Gly175Asp Single submitter ⚠
p.Gly180Asp Single submitter ⚠
p.Gly208Arg Single submitter ⚠
p.Gly245Trp Single submitter ⚠
p.Gly284Asp Single submitter ⚠
p.Gly8Arg Single submitter ⚠
p.Gly929_Val930insTer Single submitter
p.His1068Pro Single submitter ⚠
p.His1473Tyr Single submitter ⚠
p.His936Asp Single submitter ⚠
p.Ile1158Val Single submitter ⚠
p.Ile1226Val Single submitter ⚠
p.Ile617Val Single submitter ⚠
p.Ile878Val Single submitter ⚠
p.Leu1211Phe Single submitter ⚠
p.Leu1264Val Single submitter ⚠
p.Leu1425Ser Single submitter ⚠
p.Leu1448Phe Single submitter ⚠
p.Leu1516Val Single submitter ⚠
p.Leu197Phe Single submitter ⚠
p.Leu432Val Single submitter ⚠
p.Leu836Pro Single submitter ⚠
p.Leu836Val Single submitter ⚠
p.Lys1029Arg Single submitter ⚠
p.Lys137Arg Single submitter ⚠
p.Lys1525Arg Single submitter ⚠
p.Lys1562Glu Single submitter ⚠
p.Lys1660Glu Single submitter ⚠
p.Lys189Gln Single submitter ⚠
p.Lys258Ile Single submitter ⚠
p.Lys416Glu Single submitter ⚠
p.Lys425Asn Single submitter ⚠
p.Lys757Arg Single submitter ⚠
p.Lys895Thr Single submitter ⚠
p.Lys995Gln Single submitter ⚠
p.Met1283Ile Single submitter ⚠
p.Met1283Thr Single submitter ⚠
p.Met1283Val Single submitter ⚠
p.Met1449Thr Single submitter ⚠
p.Met1484Arg Single submitter ⚠
p.Met253Val Single submitter ⚠
p.Met369Val Single submitter ⚠
p.Met880Thr Single submitter ⚠
p.Phe130Ser Single submitter ⚠
p.Phe1480Leu Single submitter ⚠
p.Phe22Ser Single submitter ⚠
p.Phe321Cys Single submitter ⚠
p.Phe35Leu Single submitter KDM5A-related disorder ⚠
p.Pro1109Ser Single submitter ⚠
p.Pro1420Thr Single submitter ⚠
p.Pro1424Ser Single submitter ⚠
p.Pro1432Leu Single submitter ⚠
p.Pro1433Leu Single submitter ⚠
p.Pro1433Ser Single submitter ⚠
p.Pro1493Leu Single submitter ⚠
p.Pro150Arg Single submitter ⚠
p.Pro1667Ala Single submitter ⚠
p.Pro1682Leu Single submitter ⚠
p.Pro328Ser Single submitter ⚠
p.Pro6Leu Single submitter ⚠
p.Pro889Leu Single submitter ⚠
p.Pro967Leu Single submitter ⚠
p.Ser1027Cys Single submitter ⚠
p.Ser103Cys Single submitter ⚠
p.Ser1085Asn Single submitter ⚠
p.Ser1202Arg Single submitter ⚠
p.Ser1326Asn Single submitter ⚠
p.Ser1362Ile Single submitter ⚠
p.Ser1408Asn Single submitter ⚠
p.Ser1413Phe Single submitter ⚠
p.Ser1458Tyr Single submitter ⚠
p.Ser1488Ile Single submitter KDM5A-related disorder ⚠
p.Ser1488Thr Single submitter ⚠
p.Ser1502Leu Single submitter ⚠
p.Ser1644Ala Single submitter ⚠
p.Ser1674Ala Single submitter ⚠
p.Ser375Tyr Single submitter ⚠
p.Ser400Arg Single submitter ⚠
p.Ser883Gly Single submitter ⚠
p.Thr104Ala Single submitter ⚠
p.Thr1057Ala Single submitter ⚠
p.Thr1069Ala Single submitter ⚠
p.Thr1343Pro Single submitter ⚠
p.Thr1415Ile Single submitter ⚠
p.Thr1462Ser Single submitter ⚠
p.Thr1472Ile Single submitter ⚠
p.Thr1580Ala Single submitter ⚠
p.Thr234Met Single submitter ⚠
p.Thr747Ile Single submitter ⚠
p.Thr950Ala Single submitter ⚠
p.Trp1256Ter Single submitter
p.Trp139Cys Single submitter ⚠
p.Trp1466Arg Single submitter ⚠
p.Trp1466fs Single submitter
p.Tyr1353His Single submitter ⚠
p.Tyr318Cys Single submitter ⚠
p.Val1043Glu Single submitter ⚠
p.Val109Ala Single submitter ⚠
p.Val1238Ile Single submitter ⚠
p.Val248Gly Single submitter ⚠
p.Val295Ala Single submitter ⚠
p.Val544Met Single submitter ⚠
p.Val552Met Single submitter ⚠
p.Val978Ala Single submitter ⚠
p.Phe477Leu No assertion criteria KDM5A-related disorder ⚠
p.Ser912Ter No assertion criteria KDM5A-related disorder
p.Tyr570Cys No assertion criteria ⚠
p.Val1324Gly No assertion criteria KDM5A-related disorder ⚠