CCBE1 — 550 ClinVar variants

All ClinVar germline CCBE1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 166 flagged for review →

12 Pathogenic · 5 Likely pathogenic · 24 Conflicting · 73 Benign · 3 Benign/Likely benign · 175 Likely benign · 258 Uncertain significance

Full CCBE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 166

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 5

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

Predictors lean, ClinVar uncertain 83

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

Predictors split 78

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

All CCBE1 variants

Pathogenic 12

Likely pathogenic 5

Conflicting classifications of pathogenicity 24

  • c.131+10G>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.213-1G>A Single submitter
  • c.265+8A>C Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.654+10G>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.654+5G>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.916-2A>G Single submitter Inborn genetic diseases
  • c.*2728A>G Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Arg118= Single submitter
  • p.Arg158Cys Single submitter CCBE1-related disorder ⚠
  • p.Arg167Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg360Gln Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1 ⚠
  • p.Arg391Lys Single submitter Inborn genetic diseases ⚠
  • p.Asp104Asn Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1 ⚠
  • p.Asp388Gly Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1 ⚠
  • p.Cys75Ser Single submitter Fetal anomalies with a likely genetic cause ⚠
  • p.Leu339= Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Lys355Thr Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1 ⚠
  • p.Pro270= Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Pro87Gln Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1 ⚠
  • p.Thr144Met Single submitter CCBE1-related disorder ⚠
  • p.Thr184= Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Thr234Ala Single submitter Inborn genetic diseases ⚠
  • p.Tyr114= Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Tyr57= Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1

Benign 73

  • c.132-148C>G Multiple submitters
  • c.212+233A>G Multiple submitters
  • c.213-209G>T Multiple submitters
  • c.265+26C>A Multiple submitters
  • c.265+28G>C Multiple submitters
  • c.265+67C>T Multiple submitters
  • c.266-104C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.266-156C>T Multiple submitters
  • c.266-30T>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.266-45C>T Multiple submitters
  • c.266-63G>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.400+165A>G Multiple submitters
  • c.401-174G>T Multiple submitters
  • c.401-225G>C Multiple submitters
  • c.401-29T>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.553+109A>T Multiple submitters
  • c.654+214A>G Multiple submitters
  • c.655-155A>T Multiple submitters
  • c.655-197C>T Multiple submitters
  • c.655-229T>C Multiple submitters
  • c.775+12A>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.775+171C>T Multiple submitters
  • c.775+82A>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.776-164G>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.952-260T>C Multiple submitters
  • c.988-10A>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*1040C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*14C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2020C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2227G>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2242T>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2361G>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2372C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2673G>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2730A>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2758C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2825A>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3036C>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3162T>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3475G>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3780A>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3805T>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4398C>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4504G>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4749C>T Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4788T>C Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4796G>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4945C>A Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*814T>G Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Arg167Trp Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1 ⚠
  • p.Asp41Glu Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Ile52= Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Pro279= Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.132-232C>A Single submitter
  • c.265+204C>T Single submitter
  • c.553+17T>A Single submitter
  • c.553+249A>G Single submitter
  • c.553+301A>T Single submitter
  • c.951+314C>T Single submitter
  • c.988-154dup Single submitter
  • c.988-179C>T Single submitter
  • c.*1258C>G Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*154G>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*1697G>C Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*1969A>G Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2787T>C Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2833C>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*2978T>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3533C>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*3777A>T Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4180A>G Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*4846G>A Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1
  • c.*616A>G Single submitter Hennekam lymphangiectasia-lymphedema syndrome 1

Benign/Likely benign 3

  • p.Glu65= Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.His186Arg Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1
  • p.Pro181Ser Multiple submitters Hennekam lymphangiectasia-lymphedema syndrome 1

Likely benign 175

Uncertain significance 258