Sugi Variant

Sugi Variant/KDM6B

KDM6B — 928 ClinVar variants

All ClinVar germline KDM6B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 465 flagged for review →

42 Pathogenic · 8 Pathogenic/Likely pathogenic · 70 Likely pathogenic · 15 Conflicting · 25 Benign · 12 Benign/Likely benign · 234 Likely benign · 522 Uncertain significance

Full KDM6B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 465

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 2

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

Predictors agree, ClinVar conflicts 13

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

Predicted LoF vs a conflicting call 1

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 367

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 367

Predictors split 82

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

All KDM6B variants

Pathogenic 42

  • p.Arg166Ter Multiple submitters neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg951Ter Multiple submitters KDM6B-related disorder
  • p.His434fs Multiple submitters neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4162_4165+1del Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4469-1G>C Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4737+2T>C Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4737+5G>A Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg1016fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg1156Ter Single submitter
  • p.Arg135Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg513fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg707fs Single submitter Inborn genetic diseases
  • p.Arg975Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Cys382Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln681Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln722fs Single submitter
  • p.Gln862Ter Single submitter Inborn genetic diseases
  • p.Glu220fs Single submitter Inborn genetic diseases
  • p.Glu503Ter Single submitter Inborn genetic diseases
  • p.Gly1389Cys Single submitter
  • p.Gly439fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ile1515fs Single submitter
  • p.Leu602fs Single submitter KDM6B-related neurodevelopmental disorder
  • p.Leu670_Phe671insTer Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Lys1101fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Lys1341Ter Single submitter
  • p.Met1373Thr Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Pro391fs Single submitter Inborn genetic diseases
  • p.Pro664fs Single submitter Inborn genetic diseases
  • p.Pro905fs Single submitter Inborn genetic diseases
  • p.Ser1364fs Single submitter
  • p.Ser1518fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ser358fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Thr760fs Single submitter
  • p.Trp1340Ter Single submitter
  • p.Trp1463Ter Single submitter Inborn genetic diseases
  • p.Trp1483Ter Single submitter
  • p.Trp1502_Glu1504delinsTer Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Tyr1189Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Tyr1432_Leu1433insTer Single submitter
  • p.Tyr1500Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Asn1584Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities

Pathogenic/Likely pathogenic 8

  • p.Arg1499Ter Multiple submitters neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg199Ter Multiple submitters neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg229Ter Multiple submitters intellectual disability
  • p.Arg495Ter Multiple submitters Neurodevelopmental delay
  • p.Cys473fs Multiple submitters KDM6B-related disorder
  • p.Glu362fs Multiple submitters neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Phe1396del Multiple submitters KDM6B-related disorder
  • p.Asp1254del No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities

Likely pathogenic 70

  • c.138-1G>A Single submitter Inborn genetic diseases
  • c.236+1G>A Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.3566_3567+6del Single submitter
  • c.3945-2A>T Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4908+25_4909-50dup Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ala956fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg11fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg1246Cys Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg1246His Single submitter Inborn genetic diseases
  • p.Arg1453Cys Single submitter Inborn genetic diseases
  • p.Arg522fs Single submitter
  • p.Asn1480del Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Cys1397Tyr Single submitter KDM6B-related disorder
  • p.Gln1391Arg Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln175Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln858Ter Single submitter KDM6B-related disorder
  • p.Gln957Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Leu519fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Leu902fs Single submitter KDM6B-related disorder
  • p.Met370_Asp371delinsArgPheThrSer Single submitter
  • p.Phe1424del Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Pro325fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Pro481fs Single submitter KDM6B-related disorder
  • p.Ser1096fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Thr1185fs Single submitter KDM6B-related disorder
  • p.Thr1434Pro Single submitter
  • p.Thr353fs Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Trp1471Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Trp1502Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Trp41Ter Single submitter KDM6B-related disorder
  • p.Tyr1491Cys Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities ⚠
  • p.Tyr188Ter Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Val535Met Single submitter neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities ⚠
  • c.138-2A>G No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.3674-2A>G No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.3944+1G>A No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4165+2T>A No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • c.4468+5G>C No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ala141fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ala352fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg1566Ser No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg340fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Arg996fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Cys1408Arg No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Cys1575Ser No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Cys1578fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln115Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln712Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gln733Ter No assertion criteria KDM6B-related disorder
  • p.Gln897fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Glu1179fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Glu1304fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Glu1392Lys No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Glu1570Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Glu709Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gly193fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gly412fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Gly421fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Leu1599fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Lys1013fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Lys991Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Phe1396Ile No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Pro590fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Pro900fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ser1094Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ser1398Tyr No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Ser867fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Trp1340_Lys1341delinsTer No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Tyr1189fs No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
  • p.Tyr816Ter No assertion criteria neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities

Conflicting classifications of pathogenicity 15

Benign 25

Benign/Likely benign 12

Likely benign 234

Uncertain significance 522

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