KMT5B — 293 ClinVar variants

All ClinVar germline KMT5B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 122 flagged for review →

32 Pathogenic · 6 Pathogenic/Likely pathogenic · 44 Likely pathogenic · 8 Conflicting · 6 Benign · 1 Benign/Likely benign · 56 Likely benign · 140 Uncertain significance

Full KMT5B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 122

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 6

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

Predicted LoF vs a conflicting call 2

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 90

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

Predictors split 24

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

All KMT5B variants

Pathogenic 32

  • p.Ala261fs Multiple submitters Inborn genetic diseases
  • p.Arg220Ter Multiple submitters Inborn genetic diseases
  • p.Arg286Ter Multiple submitters KMT5B-related disorder
  • p.Cys78_Glu79delinsTer Multiple submitters Autistic behavior
  • p.Leu242fs Multiple submitters intellectual disability, autosomal dominant 51
  • p.Lys223fs Multiple submitters intellectual disability, autosomal dominant 51
  • p.Arg699Ter Single submitter KMT5B-related disorder
  • p.Asn389fs Single submitter
  • p.Asn433fs Single submitter intellectual disability, autosomal dominant 51
  • p.Asn731fs Single submitter Inborn genetic diseases
  • p.Asn798fs Single submitter intellectual disability
  • p.Cys305fs Single submitter intellectual disability, autosomal dominant 51
  • p.Gln33fs Single submitter intellectual disability, autosomal dominant 51
  • p.Glu325Ter Single submitter intellectual disability, autosomal dominant 51
  • p.Glu471Ter Single submitter intellectual disability, autosomal dominant 51
  • p.Gly576fs Single submitter intellectual disability, autosomal dominant 51
  • p.Gly608fs Single submitter intellectual disability, autosomal dominant 51
  • p.His512fs Single submitter intellectual disability, autosomal dominant 51
  • p.Lys403fs Single submitter intellectual disability, autosomal dominant 51
  • p.Lys491Ter Single submitter intellectual disability, autosomal dominant 51
  • p.Ser110Ter Single submitter intellectual disability, autosomal dominant 51
  • p.Ser614fs Single submitter KMT5B & SUV420H1-related disorders
  • p.Ser726fs Single submitter
  • p.Thr97fs Single submitter
  • p.Tyr203Ter Single submitter intellectual disability
  • p.Tyr791Ter Single submitter Inborn genetic diseases
  • p.Val252fs Single submitter intellectual disability, autosomal dominant 51
  • p.Ala74fs No assertion criteria intellectual disability, autosomal dominant 51
  • p.Asn278Ile No assertion criteria intellectual disability, autosomal dominant 51
  • p.Asn520fs No assertion criteria intellectual disability, autosomal dominant 51
  • p.His181Asp No assertion criteria intellectual disability, autosomal dominant 51
  • p.Ser86fs No assertion criteria intellectual disability, autosomal dominant 51

Pathogenic/Likely pathogenic 6

  • c.840+1_840+5del Multiple submitters intellectual disability, autosomal dominant 51
  • p.Arg187Ter Multiple submitters intellectual disability, autosomal dominant 51
  • p.Arg395Ter Multiple submitters intellectual disability, autosomal dominant 51
  • p.Arg783Ter Multiple submitters intellectual disability, autosomal dominant 51
  • p.Leu808fs Multiple submitters intellectual disability, autosomal dominant 51
  • p.Tyr185fs Multiple submitters intellectual disability, autosomal dominant 51

Likely pathogenic 44

Conflicting classifications of pathogenicity 8

Benign 6

Benign/Likely benign 1

Likely benign 56

Uncertain significance 140