Variant classification summary

NM_001098209.2:c.98C>A

CTNNB1 · NP_001091679.1:p.(Ser33Tyr) · NM_001098209.2

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

Gene: CTNNB1 Transcript: NM_001098209.2

Final call

Pathogenic

PS3 strong PM1 moderate PM2 moderate PM5 moderate BP4 supporting benign

Variant details

Gene

CTNNB1

Transcript

NM_001098209.2

Protein

NP_001091679.1:p.(Ser33Tyr)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

Absent from all gnomAD population databases including v2.1, v4.1, and gnomAD-Canada.

2

Located at serine 33, a critical GSK-3beta phosphorylation site within the N-terminal degradation domain of beta-catenin, identified as a statistically significant hotspot residue.

3

Functional studies demonstrate that p.Ser33Tyr causes gain-of-function through constitutive beta-catenin stabilization and enhanced TCF-mediated transcriptional activation, tested directly in T-LBL/ALL cell lines and Huh7 luciferase reporter assays.

4

Different pathogenic missense changes at the same codon (S33F, S33C) have been established as pathogenic in multiple independent publications across pilomatricomas, medulloblastomas, and T-cell malignancies.

5

In silico prediction tools (REVEL 0.495, BayesDel 0.0085, SpliceAI 0.00) do not support a damaging effect, though this is outweighed by the strong functional evidence.

6

This variant has been reported in somatic cancers 103 times in COSMIC and is classified as Oncogenic (gain-of-function) by OncoKB.

7

Applying generic ACMG/AMP 2015 combination rules: PS3 (strong) + PM1 (moderate) + PM2 (moderate) + PM5 (moderate) + BP4 (supporting benign) = 1 strong + 3 moderate pathogenic criteria minus 1 supporting benign criterion. This combination meets the threshold for Pathogenic classification.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

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	PVS1 is not applicable to missense substitutions. This is a missense variant (c.98C>A, p.Ser33Tyr), not a null variant (nonsense, frameshift, or canonical splice site). The generic PVS1 framework requires null-variant buckets; variant fell into 'other' bucket with apply_generic_pvs1_framework=false.
PS1	N/A	PS1 requires a different nucleotide change producing the same amino acid change as a previously established pathogenic variant. At codon 33, TCT→TAT is the only nucleotide substitution yielding tyrosine; no alternative nucleotide change produces p.Ser33Tyr.
PS2	Not met	No de novo occurrence data were identified for NM_001098209.2:c.98C>A in any reviewed publication or database source. Confirmed de novo status requires parental testing, which is absent from the available evidence.
PS3	Met	The exact variant p.Ser33Tyr has been directly tested in functional assays in at least two independent publications. Groen et al. (2008, PMID:18757411) identified S33Y in a primary T-LBL/ALL and demonstrated that S33Y h-catenin transfection into T-LBL/ALL cell lines enhanced TCF-mediated transcription and promoted cell growth. Pilati et al. (2014, PMID:24735922) tested S33Y in a TOP-FLASH luciferase reporter assay in Huh7 cells, confirming strong activation of beta-catenin transcriptional activity. Both studies demonstrate unequivocal gain-of-function: the variant disrupts the GSK-3beta phosphorylation site at serine 33, preventing ubiquitin-mediated degradation and causing constitutive beta-catenin stabilization and transcriptional activation.	PMID:18757411 PMID:24735922
PS4	Not met	No germline case-control data or observational cohort data are available for this variant. COSMIC reports 103 somatic observations, but these do not constitute germline case observations. No affected individual counts from clinical testing cohorts are available.
PS5	Not met	The variant p.Ser33Tyr is reported as Pathogenic in ClinVar (VariationID 17577) but with review status 'no assertion criteria provided' (1-star), submitted by OMIM via literature-only method with somatic origin. This does not meet the 'reputable source' threshold required for PS5 under generic ACMG/AMP. Additionally, PS5 typically applies when a different nucleotide change produces the same amino acid change as a known pathogenic variant; no alternative nucleotide change exists for p.Ser33Tyr.	clinvar
PM1	Met	The variant is located at codon 33 (serine 33), one of the four critical GSK-3beta phosphorylation sites (S33, S37, T41, S45) within the N-terminal degradation domain of beta-catenin (amino acids 29-49). This domain is essential for ubiquitin-mediated degradation of beta-catenin. Mutations at these residues are well-established to cause beta-catenin stabilization and constitutive WNT pathway activation. Cancer Hotspots identifies this residue as statistically significant. The N-terminal domain is a well-characterized functional domain critical to beta-catenin regulation.	PMID:10192393 PMID:18757411
PM2	Met	This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 across all populations. The complete absence from large population databases supports pathogenicity.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Met	Multiple different missense changes at codon 33 have been reported as pathogenic in the literature and ClinVar. Specifically, S33F (TCT→TTT) and S33C (TCT→TGT) are established pathogenic variants at the same residue. S33F was reported in pilomatricomas (PMID:10192393, 2 cases), medulloblastomas (PMID:16685513, 3 cases; PMID:16258095, codon 33 TCT→TTT; SER→PHE), and T-cell lymphoma (PMID:18757411, 1 case). S33C was reported in medulloblastomas (PMID:16685513, 2 cases). These same-residue comparator variants with different amino acid changes satisfy PM5 under generic ACMG/AMP.	PMID:10192393 PMID:16258095 PMID:16685513 PMID:18757411
PM6	Not met	No de novo occurrence data were identified for NM_001098209.2:c.98C>A in any reviewed publication. Confirmed de novo status requires parental testing, which is absent from the available evidence.
PP1	Not met	No cosegregation data are available for this variant. No family studies with affected and unaffected members were identified in the reviewed literature.
PP2	Not met	While CTNNB1 has a significant number of pathogenic missense variants in exon 3, the primary germline disease mechanism for CTNNB1 syndrome (MIM 615075) is loss-of-function via nonsense and frameshift variants. Missense variants in exon 3 are predominantly associated with somatic gain-of-function in cancer. The HCI prior score is unavailable for CTNNB1. PP2 is not met under generic ACMG/AMP because missense is not the predominant mechanism for the established germline disease.
PP3	Not met	In silico prediction tools do not support a damaging effect for this variant. REVEL score is 0.495 (below the typical 0.5 threshold). BayesDel score is 0.0085 (very low, not consistent with pathogenicity). SpliceAI max delta score is 0.00 (no predicted splicing impact). Multiple lines of computational evidence do not support a deleterious effect.	revel bayesdel spliceai
PP4	Not assessed	No patient phenotype or specific clinical data were available for this case. PP4 requires phenotype specificity or family history consistent with the gene-associated condition.
PP5	Not met	ClinVar reports this variant as Pathogenic (VariationID 17577) but with review status 'no assertion criteria provided' (1-star), submitted by OMIM via literature-only method with somatic origin. The global PP5 rule requires ClinVar 3-star expert panel review to apply at supporting strength. The current 1-star status does not meet the threshold for PP5 under generic ACMG/AMP.	clinvar
BA1	Not met	The variant is absent from all gnomAD populations (v2.1, v4.1, Canada v1.0). The allele frequency is 0.00, well below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is absent from all gnomAD populations (v2.1, v4.1, Canada v1.0). The allele frequency is 0.00, well below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data are available regarding observation of this variant in healthy adults. BS2 requires documented observation in a healthy adult individual with full penetrance expected at an early age.
BS3	Not met	Multiple functional studies demonstrate that p.Ser33Tyr is a gain-of-function variant causing constitutive beta-catenin stabilization and transcriptional activation. In T-LBL/ALL cell lines, S33Y expression enhanced TCF-mediated transcription and promoted cell growth (PMID:18757411). In Huh7 cells, S33Y strongly activated a beta-catenin-driven luciferase reporter (PMID:24735922). These findings are consistent with a damaging, not benign, functional effect.	PMID:18757411 PMID:24735922
BS4	Not met	No cosegregation data are available for this variant. BS4 requires lack of segregation in affected family members.
BP1	Not met	Although CTNNB1 syndrome (MIM 615075) is predominantly caused by truncating loss-of-function variants, the variant p.Ser33Tyr is located at a critical GSK-3beta phosphorylation site within the N-terminal degradation domain. Serine 33 is one of four residues whose phosphorylation is essential for beta-catenin ubiquitination and degradation. Missense changes at this residue are a well-established gain-of-function mechanism demonstrated in multiple functional studies. BP1 is not applied when the missense variant affects a known critical functional residue.	PMID:10192393 PMID:18757411
BP2	N/A	No evidence of observation in trans with a pathogenic variant. BP2 is not applicable in the absence of phase data.
BP4	Met	Multiple lines of computational evidence suggest a lack of deleterious effect. REVEL score is 0.495, below the typical 0.5 pathogenic threshold. BayesDel score is 0.0085, a very low value not consistent with damaging effect. SpliceAI max delta score is 0.00, indicating no predicted impact on splicing. While REVEL is borderline, the consensus of three independent in silico predictors leans toward a benign interpretation.	revel bayesdel spliceai
BP5	Not met	The variant is reported as Pathogenic in ClinVar (VariationID 17577), not benign. BP5 requires a reputable source to report the variant as benign or likely benign, which is not the case here.	clinvar
BP6	N/A	ClinVar reports this variant as Pathogenic, not benign. BP6 requires a reputable source to report the variant as benign.
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. NM_001098209.2:c.98C>A is a missense variant (p.Ser33Tyr), not a synonymous variant.

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