CTNNB1 — 855 ClinVar variants

All ClinVar germline CTNNB1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 303 flagged for review →

151 Pathogenic · 8 Pathogenic/Likely pathogenic · 55 Likely pathogenic · 15 Conflicting · 23 Benign · 10 Benign/Likely benign · 281 Likely benign · 312 Uncertain significance

Full CTNNB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 303

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 7

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 199

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 199

Predictors split 93

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

All CTNNB1 variants

Pathogenic 151

  • c.1081+1G>T Multiple submitters colorectal cancer
  • c.1082-1G>C Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • c.735-1G>C Multiple submitters colorectal cancer
  • p.Arg515Ter Multiple submitters hepatocellular carcinoma
  • p.Arg535Ter Multiple submitters exudative vitreoretinopathy 7
  • p.Arg661fs Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Arg95Ter Multiple submitters CTNNB1-related disorder
  • p.Asp695fs Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln113Ter Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln395Ter Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln530Ter Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln623Ter Multiple submitters
  • p.Gln92Ter Multiple submitters
  • p.His499fs Multiple submitters hepatocellular carcinoma
  • p.Ile140fs Multiple submitters
  • p.Leu385fs Multiple submitters
  • p.Met271fs Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr289fs Multiple submitters CTNNB1-related disorder
  • p.Tyr333Ter Multiple submitters CTNNB1-related disorder
  • p.Tyr654Ter Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Val349fs Multiple submitters hepatocellular carcinoma
  • c.1081+1G>A Single submitter Inborn genetic diseases
  • c.1081+1G>C Single submitter
  • c.1082-2A>G Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1683+1G>A Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1683+1G>C Single submitter
  • c.2076+1G>A Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.2076+2T>C Single submitter
  • c.242-1G>T Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.242-2A>G Single submitter
  • c.242-3C>A Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.495+1G>C Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.735-1G>A Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.937-2A>G Single submitter
  • p.Ala269fs Single submitter Inborn genetic diseases
  • p.Ala421fs Single submitter
  • p.Ala615Ter Single submitter
  • p.Ala622fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Ala657fs Single submitter
  • p.Ala96fs Single submitter
  • p.Arg185fs Single submitter intellectual disability
  • p.Arg185Ter Single submitter
  • p.Asn380fs Single submitter
  • p.Asn387fs Single submitter Inborn genetic diseases
  • p.Asn434fs Single submitter
  • p.Asp32Asn Single submitter juvenile nasopharyngeal angiofibroma
  • p.Asp624fs Single submitter Inborn genetic diseases
  • p.Asp669fs Single submitter
  • p.Asp713fs Single submitter
  • p.Cys381fs Single submitter
  • p.Gln123fs Single submitter
  • p.Gln123Ter Single submitter
  • p.Gln165fs Single submitter
  • p.Gln177Ter Single submitter Inborn genetic diseases
  • p.Gln266Ter Single submitter Inborn genetic diseases
  • p.Gln309fs Single submitter
  • p.Gln364Ter Single submitter
  • p.Gln379Ter Single submitter Inborn genetic diseases
  • p.Gln482Ter Single submitter
  • p.Gln538Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln548Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln601Ter Single submitter
  • p.Gln61Ter Single submitter
  • p.Gln72fs Single submitter
  • p.Gln85fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu310Ter Single submitter
  • p.Glu334fs Single submitter CTNNB1-related disorder
  • p.Glu54Ter Single submitter
  • p.Glu55Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu620fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu634Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu642fs Single submitter
  • p.Glu642Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu705fs Single submitter
  • p.Gly319fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Ile315fs Single submitter intellectual disability
  • p.Ile590fs Single submitter intellectual disability
  • p.Ile610fs Single submitter exudative vitreoretinopathy 7
  • p.Leu244fs Single submitter
  • p.Leu259fs Single submitter
  • p.Leu263fs Single submitter
  • p.Leu263Ter Single submitter Inborn genetic diseases
  • p.Leu264fs Single submitter
  • p.Leu366Ter Single submitter CTNNB1-related disorder
  • p.Leu424_Ser425insTer Single submitter
  • p.Leu452fs Single submitter
  • p.Leu527Ter Single submitter
  • p.Leu659fs Single submitter
  • p.Leu707fs Single submitter
  • p.Lys158_Leu159insMetMetGlnAsnLeuProHisValGlnSerLeuAsnTerLys Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Lys181fs Single submitter
  • p.Lys270Ter Single submitter
  • p.Lys281Ter Single submitter
  • p.Lys345Ter Single submitter
  • p.Lys433Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Lys496fs Single submitter Neurodevelopmental delay
  • p.Lys496Ter Single submitter
  • p.Lys625Ter Single submitter
  • p.Met189fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Met328fs Single submitter
  • p.Phe232fs Single submitter
  • p.Phe293fs Single submitter
  • p.Pro100fs Single submitter
  • p.Pro321fs Single submitter
  • p.Pro501fs Single submitter CTNNB1-related disorder
  • p.Pro526fs Single submitter Inborn genetic diseases
  • p.Pro597fs Single submitter
  • p.Pro706fs Single submitter
  • p.Pro714fs Single submitter
  • p.Ser23fs Single submitter
  • p.Ser348fs Single submitter
  • p.Ser45fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Ser715fs Single submitter
  • p.Ser71fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr102_Leu103insTer Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr157fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr217fs Single submitter
  • p.Thr332_Tyr333insTer Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr428fs Single submitter
  • p.Thr510fs Single submitter
  • p.Thr595fs Single submitter Inborn genetic diseases
  • p.Trp338Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Trp504fs Single submitter
  • p.Trp504Ter Single submitter
  • p.Trp66Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Trp690Ter Single submitter
  • p.Tyr254Ter Single submitter
  • p.Tyr604fs Single submitter intellectual disability
  • p.Tyr654fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Tyr670fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Tyr709fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Val451fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Val493fs Single submitter
  • p.Val570Ter Single submitter
  • p.Val613fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Val617fs Single submitter Inborn genetic diseases
  • c.1683+1del No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • c.735-22_747del No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Ala636fs No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln28fs No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln309Ter No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu479fs No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gly216Arg No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gly236fs No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gly34Arg No assertion criteria urinary bladder cancer
  • p.Gly708fs No assertion criteria CTNNB1-related disorder
  • p.His720Ter No assertion criteria exudative vitreoretinopathy 7
  • p.Ile569fs No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Ser33Tyr No assertion criteria pilomatrixoma
  • p.Ser37Phe No assertion criteria pilomatrixoma
  • p.Ser425fs No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome

Pathogenic/Likely pathogenic 8

  • p.Arg587Ter Multiple submitters Inborn genetic diseases
  • p.Arg661Ter Multiple submitters Inborn genetic diseases
  • p.Gly575Arg Multiple submitters CTNNB1-related disorder
  • p.Lys233Ter Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Met437fs Multiple submitters severe intellectual disability-progressive spastic diplegia syndrome
  • p.Asp32Gly No assertion criteria pilomatrixoma ⚠
  • p.Ser37Cys No assertion criteria ovarian neoplasm
  • p.Ser45Pro No assertion criteria hepatocellular carcinoma ⚠

Likely pathogenic 55

  • p.Leu382Pro Multiple submitters Inborn genetic diseases
  • p.Thr41Ala Multiple submitters exudative vitreoretinopathy 7 ⚠
  • c.1081+2T>G Single submitter
  • c.1082-1G>A Single submitter exudative vitreoretinopathy 7
  • c.1186-1G>A Single submitter
  • c.1186-3T>G Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1524_1524+5del Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1524+1G>T Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1525-2A>G Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1803+2T>G Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1954+1G>A Single submitter CTNNB1-related disorder
  • c.241+1del Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.242-5T>G Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.496-2A>G Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.496-3C>G Single submitter
  • c.936+1G>T Single submitter
  • p.Ala481fs Single submitter
  • p.Ala694fs Single submitter
  • p.Asn308fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Asn380Ile Single submitter Inborn genetic diseases
  • p.Asn691fs Single submitter Inborn genetic diseases
  • p.Cys429Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Cys439fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Cys619_Glu620delinsTer Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln440Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln476Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Glu626Ter Single submitter microcephaly
  • p.Glu692Asp Single submitter CTNNB1-related disorder ⚠
  • p.Glu736fs Single submitter Neurodevelopmental abnormality
  • p.Gly235Arg Single submitter
  • p.Gly34Val Single submitter colorectal cancer
  • p.His36Pro Single submitter Desmoid disease, hereditary ⚠
  • p.His758fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Leu125Ter Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Leu218Ter Single submitter
  • p.Leu385Arg Single submitter
  • p.Leu517_Asn523del Single submitter
  • p.Leu598fs Single submitter congenital nervous system disorder
  • p.Met243fs Single submitter CTNNB1-related disorder
  • p.Pro373fs Single submitter CTNNB1-related syndromic intellectual disability
  • p.Ser348Phe Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr339_Arg342delinsIle Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr393_Lys394insTer Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • p.Thr393Ala Single submitter
  • p.Thr41Ile Single submitter Desmoid disease, hereditary
  • p.Tyr30_Ser37del Single submitter juvenile nasopharyngeal angiofibroma
  • p.Tyr432_Lys433delinsTer Single submitter colorectal cancer
  • p.Val511fs Single submitter hepatocellular carcinoma
  • p.Val564fs Single submitter severe intellectual disability-progressive spastic diplegia syndrome
  • c.1_1081del No assertion criteria severe intellectual disability-progressive spastic diplegia syndrome
  • p.Gln482Glu No assertion criteria colorectal cancer
  • p.Glu571Lys No assertion criteria
  • p.Gly38fs No assertion criteria CTNNB1-related disorder
  • p.Gly730Asp No assertion criteria autosomal dominant polycystic liver disease ⚠
  • p.Val406fs No assertion criteria CTNNB1-related disorder

Conflicting classifications of pathogenicity 15

Benign 23

Benign/Likely benign 10

Likely benign 281

Uncertain significance 312

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