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CTNNB1
Final classification
VUS
CTNNB1 c.98C>T · p.Ser33Phe
CTNNB1

PM1 (moderate): The variant alters serine 33, a critical GSK-3β phosphorylation residue within the N-terminal degron motif of β-catenin — a well-established functional domain where missense mutations cause constitutive Wnt pathway activation. The residue is identified as a statistically significant mutational hotspot.

Gene
CTNNB1
Transcript
NM_001098209.2
HGVS · transcript:coding
NM_001098209.2:c.98C>T
Consequence
N/A
GRCh38
chr3:41224610 C>T
GRCh37
chr3:41266101 C>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: PS3 supporting, PM1 moderate, PM2 moderate; combination = 2 moderate + 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: PS3 supporting, PM1 moderate, PM2 moderate; combination = 2 moderate + 1 supporting, which maps to VUS.
Classification rationale
PS3PM1PM2 VUS
CTNNB1 c.98C>T

PM1 (moderate): The variant alters serine 33, a critical GSK-3β phosphorylation residue within the N-terminal degron motif of β-catenin — a well-established functional domain where missense mutations cause constitutive Wnt pathway activation. The residue is identified as a statistically significant mutational hotspot.1 PM2 (moderate): The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with a variant not tolerated in the general population.2 PS3 (supporting): Functional studies demonstrate that S33F disrupts GSK-3β phosphorylation, leading to β-catenin stabilization and nuclear accumulation. In colorectal cancer tissue, the mutation was confirmed to cause increased β-catenin protein expression.3 The combined evidence (PM1 + PM2 + PS3) yields two moderate and one supporting criterion. Per ACMG/AMP 2015 generic combination rules (PMID:25741868), this does not reach the Likely Pathogenic threshold, which requires ≥3 moderate or ≥2 moderate plus ≥2 supporting criteria. The variant is classified as a Variant of Uncertain Significance (VUS).4 This variant (S33F) is a well-established somatic oncogenic driver in multiple cancer types (COSMIC count: 199; pilomatricoma, medulloblastoma, colorectal cancer, hepatocellular carcinoma) but has not been reported as a germline disease-causing variant. It is absent from population databases. Germline CTNNB1 syndrome is primarily associated with loss-of-function truncating variants, not the exon 3 degron missense mutations that characterize somatic oncogenesis.5

PS3 + PM1 + PM2 VUS
Gene diagram · NM_001098209.2 · variants mapped to exon structure
CTNNB1 NM_001098209.2
Fetching transcript structure from UCSC…
Applied criteria · 3 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
      This variant is absent from gnomAD-Canada.
      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 as other (1 clinical laboratory). (ClinVarID = 17583)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.534. BayesDel score = 0.149736.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV62688300, n = 199 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
      Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      β-Catenin accumulation and S33F mutation of CTNNB1 gene in colorectal cancer in Saudi Arabia.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met PS3 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 6 PMIDs not cited in assessment
      16685513 ↗ Stratification of medulloblastoma on the basis of histopathological grading. ONCOKB
      18467159 ↗ Chromosome instability in human hepatocellular carcinoma depends on p53 status and aflatoxin exposure. ONCOKB
      41629672 ↗ Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling. ONCOKB
      10192393 ↗ A common human skin tumour is caused by activating mutations in beta-catenin. CLINVAR
      21163964 ↗ The genetic landscape of the childhood cancer medulloblastoma. CLINVAR
      22142829 ↗ Oncogene mutation profiling of pediatric solid tumors reveals significant subsets of embryonal rhabdomyosarcoma and neuroblastoma with mutated genes in growth signaling pathways. CLINVAR