Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
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 applied · 15 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PS3 supporting Pathogenic
Functional studies demonstrate that the S33F substitution disrupts the GSK-3β phosphorylation degron motif in β-catenin, leading to protein stabilization and nuclear accumulation. In colorectal cancer tissue harboring this mutation, immunohistochemistry confirmed increased β-catenin protein expression in tumor cells versus normal adjacent tissue. S33 is a well-characterized phosphorylation site whose mutation activates canonical Wnt signaling.
Alomar et al. (2016) demonstrated S33F causes β-catenin nuclear accumulation in colorectal cancer via IHC.OncoKB classifies S33F as Likely Oncogenic with Gain-of-function mechanism.S33 is a known GSK-3β phosphorylation site in the β-catenin degron motif
PM1 moderate Pathogenic
The variant alters serine 33, a critical residue within the GSK-3β phosphorylation degron motif (residues 33-45) of β-catenin. This is a well-established functional domain where missense mutations cause constitutive Wnt pathway activation. The residue is identified as a statistically significant mutational hotspot in cancer.
Cancer Hotspots identifies S33 as a statistically significant hotspot residue.S33 is a GSK-3β phosphorylation site within the N-terminal degron motif critical for β-catenin degradation.Chang et al. (2015) identify CTNNB1 as harboring recurrent hotspot mutations.
PM2 moderate Pathogenic
The variant is absent from all population databases, including gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0, consistent with a variant not tolerated in the general population.
Absent from gnomAD v2.1.Absent from gnomAD v4.1.Absent from gnomAD-Canada v1.0.
Assessed · not applied
Pathogenic
PS2 No de novo occurrence with confirmed maternity and paternity has been reported for this variant.
PS4 No systematic case-control study comparing variant prevalence in affected individuals versus controls has been conducted.
PM6 No de novo occurrence (without confirmation of maternity/paternity) has been reported for this variant.
PP1 No segregation data are available for this variant.
PP2 CTNNB1 germline disease (CTNNB1 syndrome) is primarily caused by truncating variants, while missense variants in the degron motif are characterized as somatic oncogenic drivers.
PP3 In silico predictions are mixed and do not provide consistent support for pathogenicity.
PP4 No patient phenotype or family history information was provided for this case.
PP5 ClinVar lists this variant under variation ID 17583 with an aggregate classification of 'other' and review status 'no assertion criteria provided.' All four ClinVar submissions lack assertion criteria; two OMIM submissions classify as Pathogenic but are derived from literature only with somatic origin.
Benign
BA1 The variant is absent from gnomAD v2.1 and v4.1.
BS1 The variant is absent from gnomAD, with an allele frequency well below the BS1 threshold of >0.3%.
BS2 No observation of this variant in healthy adult individuals has been documented.
BS3 Well-established functional studies demonstrate that S33F has a gain-of-function activating effect, not a benign effect.
BS4 No segregation data are available to assess lack of cosegregation with disease.
BP4 Computational evidence is mixed and does not provide multiple consistent lines supporting a benign effect.
BP6 No reputable source reports this variant as benign.
N/A · 7 PVS1 · PS1 · PM5 · BP1 · BP2 · BP5 · 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
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