Starting
Initialising…
0%
CTNNB1
Final classification
VUS
CTNNB1 c.101_102delinsTT · p.Gly34Val
CTNNB1

NM_001904.3:c.101_102delGAinsTT (p.Gly34Val) is an in-frame indel in exon 3 of CTNNB1, within the well-established β-catenin degron hotspot (PM1).

Gene
CTNNB1
Transcript
NM_001904.3
HGVS · transcript:coding
NM_001904.3:c.101_102delinsTT
Consequence
N/A
GRCh38
chr3:41224613 GA>TT
GRCh37
chr3:41266104 GA>TT
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: PM1 moderate, PM2 moderate; combination = 2 moderate, 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: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
CTNNB1 c.101_102delinsTT

NM_001904.3:c.101_102delGAinsTT (p.Gly34Val) is an in-frame indel in exon 3 of CTNNB1, within the well-established β-catenin degron hotspot (PM1). This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2).1 The variant is absent from ClinVar and has no germline classification from any reputable source.2 OncoKB classifies this variant as Likely Oncogenic based on somatic cancer context; this does not constitute a germline pathogenicity assertion.3 No functional studies have been performed on the specific c.101_102delinsTT indel. The G34V protein change has been observed via SNV in somatic cancers (HCC, medulloblastoma) and demonstrates gain-of-function through impaired β-catenin degradation, but this mechanism does not clearly support germline loss-of-function pathogenicity for CTNNB1 syndrome (PS3 not met). SpliceAI predicts no significant splice impact (max delta score = 0.08), and REVEL/BayesDel scores are unavailable for this indel (PP3 not assessed).4 Two moderate criteria (PM1 + PM2) are met. Under ACMG/AMP 2015 combination rules, two moderate criteria alone do not reach the threshold for Likely Pathogenic (requires ≥3 moderate, or 1 strong + 1-2 moderate, or 2 moderate + ≥2 supporting). This variant is classified as a Variant of Uncertain Significance (VUS).5

PM1 + PM2 VUS
Gene diagram · NM_001904.3 · variants mapped to exon structure
CTNNB1 NM_001904.3
Fetching transcript structure from UCSC…
Applied criteria · 2 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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08).
      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 not previously been reported in somatic cancers (COSMIC).
      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 · 4 PMIDs not cited in assessment
      20921458 ↗ Definition of disease-risk stratification groups in childhood medulloblastoma using combined clinical, pathologic, and molecular variables. ONCOKB
      30113656 ↗ Targeted Molecular Analysis in Adrenocortical Carcinomas: A Strategy Toward Improved Personalized Prognostication. ONCOKB
      41629672 ↗ Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling. ONCOKB
      9671767 ↗ Somatic mutations of the beta-catenin gene are frequent in mouse and human hepatocellular carcinomas. ONCOKB