Starting
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CTNNB1
Final classification
VUS
CTNNB1 c.1149G>T · p.Trp383Cys
CTNNB1

The CTNNB1 c.1149G>T (p.Trp383Cys) variant has been observed in somatic cancers 12 times in COSMIC and has also been reported in ClinVar, although ClinVar submission-level classification details were not available from the retrieved record.

Gene
CTNNB1
Transcript
NM_001904.4
HGVS · transcript:coding
NM_001904.4:c.1149G>T
Consequence
N/A
GRCh38
chr3:41233408 G>T
GRCh37
chr3:41274899 G>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
CTNNB1 c.1149G>T

The CTNNB1 c.1149G>T (p.Trp383Cys) variant has been observed in somatic cancers 12 times in COSMIC and has also been reported in ClinVar, although ClinVar submission-level classification details were not available from the retrieved record.1 This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, placing its observed population frequency at 0, below the 0.1% rarity threshold used for PM2.2 In a published functional study of CTNNB1 armadillo repeat 5 and 6 substitutions, residue W383 was identified as recurrently mutated in cancer, and substitutions in this region were associated with reduced APC binding and increased downstream beta-catenin signaling, but direct functional testing of p.Trp383Cys was not established from the retrieved evidence.3 Computational findings are concerning for a missense effect, with REVEL 0.642 and BayesDel 0.287483, while SpliceAI predicts no meaningful splice effect with a maximum delta score of 0.02.4

PM2 VUS
Gene diagram · NM_001904.4 · variants mapped to exon structure
CTNNB1 NM_001904.4
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 4539790)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.642. BayesDel score = 0.287483.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV62692553, n = 12 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 6 PMIDs not cited in assessment
      15579438 ↗ CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors. CLINVAR
      31857074 ↗ Oncogenic Mutations in Armadillo Repeats 5 and 6 of β-Catenin Reduce Binding to APC, Increasing Signaling and Transcription of Target Genes. CLINVAR
      35101336 ↗ Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). CLINVAR
      22918138 ↗ Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. CLINVAR
      34131312 ↗ Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
      23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR