Variant classification summary

NM_001098209.2:c.98C>T

CTNNB1 · NP_001091679.1:p.(Ser33Phe) · NM_001098209.2

GRCh37: chr3:41266101 C>T · GRCh38: chr3:41224610 C>T

Gene: CTNNB1 Transcript: NM_001098209.2

Final call

VUS

PS3 supporting PM1 moderate PM2 moderate

Variant details

Gene

CTNNB1

Transcript

NM_001098209.2

Protein

NP_001091679.1:p.(Ser33Phe)

gnomAD AF

ClinVar

other

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

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).

5

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.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This is a missense variant (c.98C>T, p.S33F). PVS1 is applicable only to null variants (nonsense, frameshift, canonical ±1,2 splice sites). The pvs1_variant_assessment confirms variant_bucket='other' and apply_generic_pvs1_framework=false.	pvs1_variant_assessment pvs1_generic_framework
PS1	N/A	No alternative nucleotide change at codon 33 resulting in the same p.S33F amino acid substitution has been identified. The only route to phenylalanine from serine at this position is c.98C>T.
PS2	Not met	No de novo occurrence with confirmed maternity and paternity has been reported for this variant.
PS3	Met	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.	PMID:27543871 oncokb
PS4	Not met	No systematic case-control study comparing variant prevalence in affected individuals versus controls has been conducted. The variant is absent from gnomAD, but no statistically significant enrichment in a well-defined patient cohort is available.	gnomad_v2 gnomad_v4
PS5	Not assessed	No evidence for an alternate molecular basis of disease in a patient carrying this variant was identified.
PM1	Met	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.	PMID:27543871 PMID:26619011
PM2	Met	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.	gnomad_v2 gnomad_v4
PM5	N/A	No same-residue comparator variant with a different pathogenic missense change was identified in ClinVar. The pm5_candidates harvest found zero eligible candidates.	pm5_candidates
PM6	Not met	No de novo occurrence (without confirmation of maternity/paternity) has been reported for this variant.
PP1	Not met	No segregation data are available for this variant.
PP2	Not assessed	CTNNB1 germline disease (CTNNB1 syndrome) is primarily caused by truncating variants, while missense variants in the degron motif are characterized as somatic oncogenic drivers. The gene's germline missense constraint metrics were not evaluated in this assessment.
PP3	Not met	In silico predictions are mixed and do not provide consistent support for pathogenicity. REVEL score is 0.534 (borderline), BayesDel score is 0.150 (low, favoring benign), and SpliceAI predicts no splice impact (max delta 0.00). Multiple computational lines do not converge on a pathogenic prediction.	revel bayesdel spliceai
PP4	Not assessed	No patient phenotype or family history information was provided for this case.
PP5	Not met	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. No clinical diagnostic laboratory with supporting criteria has reported this variant as pathogenic for germline disease.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1 and v4.1. The allele frequency is 0%, far below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is absent from gnomAD, with an allele frequency well below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4
BS2	Not met	No observation of this variant in healthy adult individuals has been documented. The variant is absent from gnomAD, providing no evidence for benign occurrence in trans with a pathogenic variant or in unaffected controls.	gnomad_v2 gnomad_v4
BS3	Not met	Well-established functional studies demonstrate that S33F has a gain-of-function activating effect, not a benign effect. The substitution disrupts the GSK-3β phosphorylation degron, leading to β-catenin stabilization and constitutive Wnt signaling.	PMID:27543871 oncokb
BS4	Not met	No segregation data are available to assess lack of cosegregation with disease.
BP1	N/A	Missense variants in the CTNNB1 degron motif are a well-established mechanism of pathogenicity (gain-of-function). BP1 applies only when missense variants are not a known disease mechanism for the gene.	PMID:27543871 oncokb
BP2	N/A	No observation in trans with a pathogenic variant in a dominant disorder has been reported. No data available to evaluate this criterion.
BP4	Not met	Computational evidence is mixed and does not provide multiple consistent lines supporting a benign effect. REVEL (0.534) is borderline pathogenic. BayesDel (0.150) is low but not definitively benign. SpliceAI predicts no splice impact, but this alone is insufficient for BP4 in the context of a missense variant.	revel bayesdel spliceai
BP5	N/A	No alternate molecular basis for disease has been identified in a patient carrying this variant.
BP6	Not met	No reputable source reports this variant as benign. ClinVar classification is 'other' with no assertion criteria provided.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted splice impact. This is a missense variant (c.98C>T, p.S33F), not a synonymous variant.

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