Sugi Variant

Sugi Variant/CDK13

CDK13 — 1135 ClinVar variants

All ClinVar germline CDK13 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 563 flagged for review →

37 Pathogenic · 12 Pathogenic/Likely pathogenic · 36 Likely pathogenic · 59 Conflicting · 78 Benign · 29 Benign/Likely benign · 330 Likely benign · 554 Uncertain significance

Full CDK13 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 563

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 31

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

Predicted LoF vs a conflicting call 9

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 280

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 280

Predictors split 241

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 241

All CDK13 variants

Pathogenic 37

  • p.Arg737Cys Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gln152Ter Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Glu906Lys Multiple submitters Inborn genetic diseases
  • p.Gly714Asp Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gly717Arg Multiple submitters Inborn genetic diseases
  • p.Ala561fs Single submitter Inborn genetic diseases
  • p.Arg118fs Single submitter
  • p.Arg301fs Single submitter Inborn genetic diseases
  • p.Arg396fs Single submitter
  • p.Arg410Ter Single submitter Inborn genetic diseases
  • p.Arg928Ter Single submitter
  • p.Arg958Ter Single submitter
  • p.Asp837Asn Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Asp837Glu Single submitter
  • p.Asp855Gly Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gln1124Ter Single submitter
  • p.Glu306Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Glu501fs Single submitter
  • p.Glu595Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Glu654fs Single submitter Inborn genetic diseases
  • p.Glu743Ter Single submitter
  • p.Gly176fs Single submitter
  • p.Gly714Arg Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gly714Val Single submitter
  • p.Leu87fs Single submitter
  • p.Lys663Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Lys677Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Lys734Glu Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Pro952fs Single submitter
  • p.Ser317fs Single submitter
  • p.Ser385fs Single submitter Inborn genetic diseases
  • p.Ser577Ter Single submitter
  • p.Tyr310Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Tyr399Ter Single submitter Inborn genetic diseases
  • p.Val564Ter Single submitter Inborn genetic diseases
  • p.Lys734Thr No assertion criteria congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Val874Leu No assertion criteria congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

Pathogenic/Likely pathogenic 12

  • p.Arg1025Ter Multiple submitters
  • p.Arg751Gln Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Arg860Gln Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Arg880Cys Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Asn842Asp Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Asn842Ser Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Asp855Tyr Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gly712Arg Multiple submitters Abnormal heart morphology
  • p.Gly857Glu Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Leu61fs Multiple submitters Inborn genetic diseases
  • p.Lys734Arg Multiple submitters CDK13-related disorder
  • p.Ser177fs Multiple submitters Inborn genetic diseases

Likely pathogenic 36

  • p.Ala732Thr Multiple submitters congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Asp855Asn Multiple submitters Neurodevelopmental abnormality
  • c.2354-1G>A Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • c.2780+152G>A Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Ala859Pro Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Arg110fs Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Arg836Gly Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Arg836Ile Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Arg958Gln Single submitter
  • p.Asp773His Single submitter neurodevelopmental disorder
  • p.Asp855His Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gln544Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Glu713Gly Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Glu775fs Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Gly714Cys Single submitter Global developmental delay
  • p.Gly857Ala Single submitter
  • p.His813_Ile814insTer Single submitter
  • p.Ile553Val Single submitter ⚠
  • p.Ile708del Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Leu674Ter Single submitter
  • p.Lys540fs Single submitter CDK13-related disorder
  • p.Lys734Asn Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Phe809fs Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Pro933Ala Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Ser1070Phe Single submitter Neurodevelopmental delay ⚠
  • p.Thr1143fs Single submitter
  • p.Thr876Ala Single submitter
  • p.Thr876Ile Single submitter
  • p.Thr988Ile Single submitter
  • p.Trp697Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Tyr300Ter Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Tyr870Cys Single submitter congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Ala749Glu No assertion criteria congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Asp837Gly No assertion criteria congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
  • p.Leu443_Thr444insTer No assertion criteria CDK13-related disorder
  • p.Ser269fs No assertion criteria congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

Conflicting classifications of pathogenicity 59

Benign 78

Benign/Likely benign 29

Likely benign 330

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

Uncertain significance 554

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