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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 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
This variant alters codon 34 (Gly34Val) within the CTNNB1 exon 3 degron hotspot (residues 31-48), a well-established mutational hotspot and critical functional domain for β-TRCP binding and β-catenin degradation. The residue lies in a statistically significant CancerHotspots region.
Alters Gly34 in the CTNNB1 degron hotspotCancerHotspots confirms statistically significant enrichment of mutations at this residue.
PM2 moderate Pathogenic
This variant is completely absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, well below the PM2 threshold of 0.1% allele frequency.
Absent from gnomAD v2.1 (0 alleles)gnomAD v4.1 (0 alleles)gnomAD-Canada (0 alleles).
Assessed · not applied
Pathogenic
PS1 The same amino acid change (G34V) has been observed via SNV in somatic cancer (medulloblastoma, HCC) but is not established as a germline pathogenic variant in ClinVar or the literature.
PS2 No de novo occurrence data are available for this variant.
PS3 Functional evidence from somatic cancer studies demonstrates that G34V (via SNV) impairs β-catenin degradation, leading to gain-of-function and Wnt pathway activation.
PS4 No case-control or prevalence data are available comparing affected versus unaffected individuals.
PM6 No de novo occurrence data are available.
PP1 No segregation data are available for this variant.
PP3 REVEL and BayesDel scores are not available for indels.
PP4 No patient phenotype or clinical data are available for evaluation of phenotype specificity.
PP5 OncoKB classifies the variant as 'Likely Oncogenic' but this is a somatic cancer designation.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No data are available on observation of this variant in healthy adult individuals for a fully penetrant disorder.
BS3 Available functional evidence demonstrates that G34V (via SNV) is activating (gain-of-function), leading to β-catenin stabilization and Wnt pathway activation.
BS4 No segregation data are available to assess lack of cosegregation with disease.
BP1 CTNNB1 germline disease (CTNNB1 syndrome / neurodevelopmental disorder with spastic diplegia and visual defects) is associated with both truncating and missense variants.
BP2 No data are available on observation of this variant in trans with a known pathogenic variant.
BP3 The variant does not lie within a repetitive region.
BP4 SpliceAI predicts no significant splice impact (max delta score = 0.08), but comprehensive in silico predictors for indels are not available.
BP5 No data are available regarding an alternate molecular basis for disease in a case harboring this variant.
BP6 No reputable source has classified this variant as benign.
N/A · 5 PVS1 · PM4 · PM5 · PP2 · BP7
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