Sugi Variant

Sugi Variant/KAT6B

KAT6B — 1757 ClinVar variants

All ClinVar germline KAT6B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 801 flagged for review →

118 Pathogenic · 7 Pathogenic/Likely pathogenic · 57 Likely pathogenic · 141 Conflicting · 72 Benign · 68 Benign/Likely benign · 519 Likely benign · 775 Uncertain significance

Full KAT6B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 801

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 3

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

Predictors agree, ClinVar conflicts 89

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

Predicted LoF vs a conflicting call 4

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 478

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 478

Predictors split 227

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 227

All KAT6B variants

Pathogenic 118

  • c.3664+1G>A Multiple submitters genitopatellar syndrome
  • p.Arg1058Ter Multiple submitters KAT6B-related disorder
  • p.Arg1797Ter Multiple submitters KAT6B-related multiple congenital anomalies syndrome
  • p.Arg352Ter Multiple submitters KAT6B-related disorder
  • p.Asn1883fs Multiple submitters KAT6B-related disorder
  • p.Gln1014Ter Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1117fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1117Ter Multiple submitters intellectual disability
  • p.Gln1194fs Multiple submitters genitopatellar syndrome
  • p.Gln1737fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1752Ter Multiple submitters genitopatellar syndrome
  • p.Gln1768Ter Multiple submitters Inborn genetic diseases
  • p.Glu1073Ter Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1085fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gly1134fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Lys1258fs Multiple submitters KAT6B-Related Spectrum Disorders
  • p.Lys1263fs Multiple submitters Inborn genetic diseases
  • p.Pro1049= Multiple submitters KAT6B-related disorder
  • p.Ser1402fs Multiple submitters KAT6B-related disorder
  • c.1993+1G>A Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • c.3021+1G>A Single submitter KAT6B-related disorder
  • c.3021+1G>T Single submitter
  • c.3022-1G>A Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • c.3373-14G>A Single submitter genitopatellar syndrome
  • c.3373-2A>C Single submitter Inborn genetic diseases
  • c.3665-1G>C Single submitter genitopatellar syndrome
  • p.Ala1331fs Single submitter genitopatellar syndrome
  • p.Ala1493fs Single submitter KAT6B-related disorder
  • p.Ala156fs Single submitter intellectual disability
  • p.Ala1621fs Single submitter genitopatellar syndrome
  • p.Ala238fs Single submitter
  • p.Arg1058fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Arg1139fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Arg1167fs Single submitter
  • p.Arg1325fs Single submitter
  • p.Arg1577fs Single submitter Inborn genetic diseases
  • p.Arg344Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Arg866= Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asn1105fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asn1531fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asn803fs Single submitter KBG syndrome
  • p.Asp1161delinsLeuTer Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asp1284fs Single submitter
  • p.Asp875fs Single submitter genitopatellar syndrome
  • p.Cys1485fs Single submitter KAT6B-related disorder
  • p.Cys837fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1014fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1040Ter Single submitter
  • p.Gln1286Ter Single submitter genitopatellar syndrome
  • p.Gln1701Ter Single submitter
  • p.Gln1716fs Single submitter genitopatellar syndrome
  • p.Gln1723fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1764Ter Single submitter genitopatellar syndrome
  • p.Gln1821Ter Single submitter genitopatellar syndrome
  • p.Glu1024fs Single submitter genitopatellar syndrome
  • p.Glu1057fs Single submitter genitopatellar syndrome
  • p.Glu1075Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1081Ter Single submitter genitopatellar syndrome
  • p.Glu1083Ter Single submitter genitopatellar syndrome
  • p.Glu1089fs Single submitter Inborn genetic diseases
  • p.Glu1095Ter Single submitter
  • p.Glu1096Ter Single submitter
  • p.Glu1099fs Single submitter
  • p.Glu1285fs Single submitter Autosomal dominant KAT6B-related disorders
  • p.Glu1363fs Single submitter Autosomal dominant KAT6B-related disorders
  • p.Glu1363Ter Single submitter
  • p.Glu1368fs Single submitter Inborn genetic diseases
  • p.Glu1371Ter Single submitter
  • p.Glu1410Ter Single submitter
  • p.Glu1413Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1510fs Single submitter genitopatellar syndrome
  • p.Glu1529fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1786Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu49Ter Single submitter intellectual disability
  • p.Glu675Ter Single submitter
  • p.Gly1921fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gly86fs Single submitter
  • p.His1433fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Leu165Ter Single submitter KAT6B-related disorder
  • p.Leu349fs Single submitter
  • p.Leu873fs Single submitter Inborn genetic diseases
  • p.Lys1124fs Single submitter
  • p.Lys1514fs Single submitter genitopatellar syndrome
  • p.Lys950fs Single submitter
  • p.Met1535fs Single submitter
  • p.Phe1127fs Single submitter KAT6B-related disorder
  • p.Phe1459_Leu1460insTer Single submitter
  • p.Phe1803fs Single submitter genitopatellar syndrome
  • p.Pro1332fs Single submitter genitopatellar syndrome
  • p.Pro1833_Tyr1834insTer Single submitter genitopatellar syndrome
  • p.Ser1041Ter Single submitter
  • p.Ser1051fs Single submitter KAT6B-related disorder
  • p.Ser1143fs Single submitter genitopatellar syndrome
  • p.Ser1303fs Single submitter genitopatellar syndrome
  • p.Ser1487fs Single submitter genitopatellar syndrome
  • p.Ser95fs Single submitter
  • p.Thr1203fs Single submitter genitopatellar syndrome
  • p.Thr1525fs Single submitter
  • p.Tyr1274Ter Single submitter genitopatellar syndrome
  • p.Tyr1680Ter Single submitter microangiopathy and leukoencephalopathy, pontine, autosomal dominant
  • p.Tyr1686Ter Single submitter neurodevelopmental disorder
  • p.Val1655fs Single submitter Inborn genetic diseases
  • p.Val713fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • c.847-2A>G No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asp1227Glufs No assertion criteria genitopatellar syndrome
  • p.Glu1007fs No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1073fs No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1356fs No assertion criteria KAT6B-related disorder
  • p.Glu1357Ter No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1411Ter No assertion criteria
  • p.Glu1454fs No assertion criteria genitopatellar syndrome
  • p.Glu1488fs No assertion criteria KAT6B-Related Spectrum Disorders
  • p.Gly1268Ter No assertion criteria genitopatellar syndrome
  • p.Gly1298Ter No assertion criteria genitopatellar syndrome
  • p.Ile1792fs No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Met1690fs No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ser1296Ter No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ser1469fs No assertion criteria blepharophimosis - intellectual disability syndrome, SBBYS type

Pathogenic/Likely pathogenic 7

  • c.1061+1G>A Multiple submitters
  • p.Arg1002Ter Multiple submitters
  • p.Arg783Ter Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1321fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ser1334fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Trp987Ter Multiple submitters KAT6B-related disorder
  • p.Val1638fs Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type

Likely pathogenic 57

  • c.2629+2T>C Single submitter
  • c.3022-1G>C Single submitter genitopatellar syndrome
  • c.3372+2T>A Single submitter genitopatellar syndrome
  • c.3373-1G>A Single submitter genitopatellar syndrome
  • p.Ala1120_Ile1121insTer Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Arg1002fs Single submitter genitopatellar syndrome
  • p.Arg1133fs Single submitter blepharophimosis
  • p.Arg591fs Single submitter
  • p.Asn1222fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asn1230fs Single submitter genitopatellar syndrome
  • p.Asn1519fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asn347fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Asp1503fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln1034delinsGlyThrArgAsnProValAsnTer Single submitter KAT6B-related disorder
  • p.Gln1286fs Single submitter genitopatellar syndrome
  • p.Gln1388Ter Single submitter Autosomal dominant KAT6B-related disorders
  • p.Gln1736Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Gln886fs Single submitter
  • p.Glu1072fs Single submitter
  • p.Glu1072Gln Single submitter ⚠
  • p.Glu1072Ter Single submitter genitopatellar syndrome
  • p.Glu1083fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1086Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1091Ter Single submitter KAT6B-related disorder
  • p.Glu1102Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1352fs Single submitter
  • p.Glu1358Ter Single submitter genitopatellar syndrome
  • p.Glu1366Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1373Ter Single submitter genitopatellar syndrome
  • p.Glu1678Ter Single submitter
  • p.Glu1681Ter Single submitter KAT6B-related disorder
  • p.His1596fs Single submitter KAT6B-related disorder
  • p.His1606fs Single submitter genitopatellar syndrome
  • p.Ile1307fs Single submitter
  • p.Ile413Thr Single submitter genitopatellar syndrome ⚠
  • p.Lys1199fs Single submitter genitopatellar syndrome
  • p.Lys250Gln Single submitter ⚠
  • p.Lys44Ter Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Met1Val Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Phe1815fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Pro1197fs Single submitter genitopatellar syndrome
  • p.Pro1809fs Single submitter genitopatellar syndrome
  • p.Ser1520fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ser1654fs Single submitter
  • p.Ser1665Gly Single submitter genitopatellar syndrome ⚠
  • p.Ser1668Gly Single submitter genitopatellar syndrome ⚠
  • p.Ser1672Gly Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type ⚠
  • p.Ser1700Ter Single submitter
  • p.Thr439fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Val1464fs Single submitter blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Val1868fs Single submitter
  • p.Arg986fs No assertion criteria KAT6B-related disorder
  • p.Glu1359fs No assertion criteria KAT6B-related disorder
  • p.Glu1364fs No assertion criteria genitopatellar syndrome
  • p.His1433Leu No assertion criteria genitopatellar syndrome ⚠
  • p.Leu1709fs No assertion criteria Chromatinopathy
  • p.Val1950fs No assertion criteria KAT6B-related disorder

Conflicting classifications of pathogenicity 141

Benign 72

Benign/Likely benign 68

  • c.2231+9A>G Multiple submitters genitopatellar syndrome
  • c.2373+6C>T Multiple submitters genitopatellar syndrome
  • c.731-11del Multiple submitters genitopatellar syndrome
  • p.Ala1037Thr Multiple submitters Inborn genetic diseases
  • p.Ala1217Ser Multiple submitters genitopatellar syndrome
  • p.Ala1426= Multiple submitters genitopatellar syndrome
  • p.Ala1493Val Multiple submitters Inborn genetic diseases
  • p.Ala1936Ser Multiple submitters Inborn genetic diseases
  • p.Ala1974= Multiple submitters genitopatellar syndrome
  • p.Arg1010Trp Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Arg1139Lys Multiple submitters genitopatellar syndrome
  • p.Arg1577His Multiple submitters Inborn genetic diseases
  • p.Arg1612His Multiple submitters genitopatellar syndrome
  • p.Arg227Cys Multiple submitters genitopatellar syndrome
  • p.Arg871Gln Multiple submitters genitopatellar syndrome ⚠
  • p.Arg960Trp Multiple submitters genitopatellar syndrome
  • p.Asn1990= Multiple submitters genitopatellar syndrome
  • p.Asp1346Tyr Multiple submitters genitopatellar syndrome
  • p.Asp1381His Multiple submitters genitopatellar syndrome
  • p.Asp1427Tyr Multiple submitters genitopatellar syndrome ⚠
  • p.Glu1104del Multiple submitters genitopatellar syndrome
  • p.Glu1104dup Multiple submitters genitopatellar syndrome
  • p.Glu1233Lys Multiple submitters genitopatellar syndrome
  • p.Glu1360= Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Glu1366_Glu1368del Multiple submitters genitopatellar syndrome
  • p.Glu1366_Glu1368dup Multiple submitters Inborn genetic diseases
  • p.Glu1367_Glu1368del Multiple submitters genitopatellar syndrome
  • p.Glu1373del Multiple submitters Inborn genetic diseases
  • p.Glu1373dup Multiple submitters genitopatellar syndrome
  • p.Glu1438Lys Multiple submitters genitopatellar syndrome
  • p.Glu233= Multiple submitters genitopatellar syndrome
  • p.Gly1134Ser Multiple submitters Inborn genetic diseases
  • p.Gly1478= Multiple submitters genitopatellar syndrome
  • p.Gly555Arg Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type ⚠
  • p.His2054= Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ile1178Thr Multiple submitters Inborn genetic diseases
  • p.Ile1537= Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ile1917Val Multiple submitters Inborn genetic diseases
  • p.Ile342Thr Multiple submitters genitopatellar syndrome ⚠
  • p.Leu1113= Multiple submitters genitopatellar syndrome
  • p.Leu1319Phe Multiple submitters genitopatellar syndrome
  • p.Leu1462Ile Multiple submitters genitopatellar syndrome
  • p.Lys1243Asn Multiple submitters genitopatellar syndrome
  • p.Pro1283Ala Multiple submitters Inborn genetic diseases
  • p.Pro1496Thr Multiple submitters genitopatellar syndrome
  • p.Pro170= Multiple submitters genitopatellar syndrome
  • p.Pro1785= Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Pro2051= Multiple submitters genitopatellar syndrome
  • p.Pro490Ser Multiple submitters genitopatellar syndrome
  • p.Pro495= Multiple submitters genitopatellar syndrome
  • p.Pro563= Multiple submitters genitopatellar syndrome
  • p.Ser1041Leu Multiple submitters Inborn genetic diseases
  • p.Ser1229Gly Multiple submitters genitopatellar syndrome
  • p.Ser125= Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ser1469= Multiple submitters blepharophimosis - intellectual disability syndrome, SBBYS type
  • p.Ser1552Arg Multiple submitters Inborn genetic diseases
  • p.Ser527Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Thr1576Asn Multiple submitters genitopatellar syndrome
  • p.Thr2016= Multiple submitters genitopatellar syndrome
  • p.Thr514Ala Multiple submitters genitopatellar syndrome
  • p.Thr552Ala Multiple submitters genitopatellar syndrome
  • p.Tyr915Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Val1464= Multiple submitters
  • p.Val1464Met Multiple submitters Inborn genetic diseases
  • p.Val1479Ile Multiple submitters genitopatellar syndrome
  • p.Val1499Ile Multiple submitters genitopatellar syndrome
  • p.Val1545Ile Multiple submitters genitopatellar syndrome
  • p.Val681Glu Multiple submitters Inborn genetic diseases

Likely benign 519

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

Uncertain significance 775

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