Sugi Variant

Sugi Variant/KAT6A

KAT6A — 2070 ClinVar variants

All ClinVar germline KAT6A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 796 flagged for review →

116 Pathogenic · 11 Pathogenic/Likely pathogenic · 85 Likely pathogenic · 132 Conflicting · 229 Benign · 102 Benign/Likely benign · 662 Likely benign · 733 Uncertain significance

Full KAT6A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 796

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 4

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 88

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

Predicted LoF vs a conflicting call 3

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 435

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 435

Predictors split 266

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 266

All KAT6A variants

Pathogenic 116

  • p.Arg1012Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg1024Ter Multiple submitters KAT6A-related disorder
  • p.Arg1129Ter Multiple submitters Inborn genetic diseases
  • p.Arg148Ter Multiple submitters Inborn genetic diseases
  • p.Arg269Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg286Ter Multiple submitters Inborn genetic diseases
  • p.Arg311Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg366Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg438Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg469Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg735Ter Multiple submitters Inborn genetic diseases
  • p.Asp1117fs Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asp503fs Multiple submitters Global developmental delay
  • p.Glu1221Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ser1458fs Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ser378Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • c.1903-5_1903-2del Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • c.2437-3C>G Single submitter
  • c.3039+1G>A Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • c.3040-1_3040del Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • c.3040-2A>C Single submitter
  • c.3353-3_3353dup Single submitter
  • c.3353-3T>G Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • c.907+1del Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ala1231fs Single submitter Inborn genetic diseases
  • p.Arg1024fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg364fs Single submitter
  • p.Asn1077fs Single submitter
  • p.Asn1836fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn277delinsArgTer Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn821fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asp1115fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asp1381Ter Single submitter
  • p.Asp1421fs Single submitter
  • p.Asp1552Val Single submitter ⚠
  • p.Cys1096fs Single submitter Inborn genetic diseases
  • p.Cys1474fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Cys393fs Single submitter
  • p.Cys626Ter Single submitter Inborn genetic diseases
  • p.Cys804Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1185Ter Single submitter
  • p.Gln1285Ter Single submitter
  • p.Gln1357Ter Single submitter intellectual disability
  • p.Gln1461Ter Single submitter
  • p.Gln1467fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1543Ter Single submitter KAT6A-related disorder
  • p.Gln1660fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln489fs Single submitter
  • p.Gln489Ter Single submitter
  • p.Gln675Ter Single submitter
  • p.Gln754Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln95fs Single submitter
  • p.Glu1050Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1107fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1139fs Single submitter
  • p.Glu1178Ter Single submitter KAT6A-related disorder
  • p.Glu1235Ter Single submitter intellectual disability
  • p.Glu1274Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1275fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1294fs Single submitter KAT6A-related disorder
  • p.Glu1300fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1325Ter Single submitter
  • p.Glu1404fs Single submitter
  • p.Glu1419fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu429fs Single submitter
  • p.Glu435fs Single submitter
  • p.Glu513Ter Single submitter
  • p.Glu823Ter Single submitter
  • p.Glu890Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gly361Ter Single submitter Inborn genetic diseases
  • p.Gly976fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.His1018fs Single submitter
  • p.His1162fs Single submitter KAT6A-related disorder
  • p.Ile1038_Ser1039insTer Single submitter Inborn genetic diseases
  • p.Ile1204fs Single submitter
  • p.Leu1061Ter Single submitter
  • p.Leu1450fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Leu493fs Single submitter
  • p.Leu596fs Single submitter intellectual disability
  • p.Leu599Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys1103fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys1134fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys126Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys1342fs Single submitter
  • p.Lys634Ter Single submitter Inborn genetic diseases
  • p.Lys636fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys709fs Single submitter Inborn genetic diseases
  • p.Lys718Ter Single submitter Inborn genetic diseases
  • p.Lys72Ter Single submitter Inborn genetic diseases
  • p.Met1849fs Single submitter
  • p.Phe1351_Leu1352insTer Single submitter
  • p.Phe615fs Single submitter
  • p.Phe744fs Single submitter
  • p.Pro1145fs Single submitter
  • p.Pro1261fs Single submitter
  • p.Ser1126fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ser1785fs Single submitter Inborn genetic diseases
  • p.Ser1856fs Single submitter
  • p.Ser1880Ter Single submitter
  • p.Ser379Ter Single submitter
  • p.Ser447Ter Single submitter Inborn genetic diseases
  • p.Ser784fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ser828Ter Single submitter
  • p.Thr1210_Val1211insTer Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Thr1455fs Single submitter
  • p.Thr1762fs Single submitter
  • p.Trp257Ter Single submitter
  • p.Trp460Ter Single submitter KAT6A-related disorder
  • p.Tyr383fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Tyr517Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Tyr523Ter Single submitter intellectual disability
  • p.Val1425fs Single submitter
  • c.3411del No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1649Ter No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln555fs No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys1148fs No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome

Pathogenic/Likely pathogenic 11

  • c.3353-1G>A Multiple submitters
  • p.Arg1019Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg148fs Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg220Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg317Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn643Ser Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1310Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1335Ter Multiple submitters KAT6A-related disorder
  • p.Gln1433Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Val1347fs Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg740fs No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome

Likely pathogenic 85

  • p.Arg251Ter Multiple submitters autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • c.2437-1G>A Single submitter
  • c.3039+1del Single submitter
  • c.3039+1G>T Single submitter
  • c.3040-1G>T Single submitter Inborn genetic diseases
  • c.3040-2A>G Single submitter
  • c.709+2T>C Single submitter
  • c.825+2T>C Single submitter
  • p.Ala1451fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ala1749_Thr1750insTer Single submitter
  • p.Ala1890fs Single submitter intellectual disability
  • p.Arg1131fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg1166fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg357Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg427Leu Single submitter ⚠
  • p.Arg765Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg982fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn1562_Tyr1563insTer Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn1708fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn277fs Single submitter KAT6A-related disorder
  • p.Asn340fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asn621Lys Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome ⚠
  • p.Asn643Asp Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Asp1092fs Single submitter KAT6A-related disorder
  • p.Asp1132fs Single submitter KAT6A-related disorder
  • p.Gln1357fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1467Ter Single submitter
  • p.Gln1607Ter Single submitter
  • p.Gln1621Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1647Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln1746fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln258Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gln912Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1062Ter Single submitter
  • p.Glu1071Ala Single submitter ⚠
  • p.Glu1222Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1248fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1262Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1275Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1292Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1297fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu541Lys Single submitter
  • p.Glu793fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gly1199fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Gly1346fs Single submitter
  • p.Gly316fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.His157Tyr Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome ⚠
  • p.Ile1512fs Single submitter KAT6A-related disorder
  • p.Ile1556Thr Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome ⚠
  • p.Ile1735fs Single submitter congenital heart disease
  • p.Ile17Thr Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ile228fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Leu51Ser Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Leu553Pro Single submitter
  • p.Leu669fs Single submitter
  • p.Leu82fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys1203fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Lys1362fs Single submitter
  • p.Lys1410fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Met1524fs Single submitter KAT6A-related disorder
  • p.Met1932Thr Single submitter ⚠
  • p.Met1Val Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Pro1683fs Single submitter KAT6A-related disorder
  • p.Pro1721fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Pro565Arg Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ser1507fs Single submitter syndromic intellectual disability
  • p.Ser1558Arg Single submitter autism spectrum disorder ⚠
  • p.Ser377Ter Single submitter KAT6A-related disorder
  • p.Ser818_His819insTer Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Thr347fs Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Trp1152Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Trp305Ter Single submitter autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Trp99Ter Single submitter
  • p.Val1882fs Single submitter
  • p.Val1901fs Single submitter neurodevelopmental disorder
  • c.3353-2_3357dup No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Arg948Ter No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1241fs No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Glu1307fs No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome
  • p.Ile1556Phe No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome ⚠
  • p.Leu606fs No assertion criteria KAT6A-related disorder
  • p.Lys1013Arg No assertion criteria ⚠
  • p.Pro528Ser No assertion criteria autism spectrum disorder
  • p.Ser1286fs No assertion criteria
  • p.Ser1555Asn No assertion criteria autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome ⚠

Conflicting classifications of pathogenicity 132

Benign 229

Benign/Likely benign 102

Likely benign 662

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 733

Showing the top 300 by review status; the full set is in the sitemap.