Is CTNNB1 p.Val511fs (c.1530dup) pathogenic?

CTNNB1 p.Val511fs (c.1530dup) is classified Likely pathogenic in CTNNB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-28). Absent from gnomAD; Associated with hepatocellular carcinoma.

What condition is associated with CTNNB1 p.Val511fs (c.1530dup)?

CTNNB1 p.Val511fs (c.1530dup) is associated with hepatocellular carcinoma (ClinVar).

How common is CTNNB1 p.Val511fs (c.1530dup) in the general population?

CTNNB1 p.Val511fs (c.1530dup) is absent from gnomAD (gnomAD).

CTNNB1 p.Val511fs

c.1530dup · rs1575330336 · VCV801962

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hepatocellular carcinoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 10 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CTNNB1
Protein: p.Val511fs
Coding: c.1530dup
MANE Select: NM_001904
dbSNP: rs1575330336
Type: Duplication
Location: chr3:41234143 (GRCh38)
Gene constraint: LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.02 · 50 PDB
Residue 511: an α-helix

Full CTNNB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hepatocellular carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CTNNB1 p.His499fs Pathogenic ★★ same condition
CTNNB1 p.Arg474Ter Pathogenic ★★ same condition
CTNNB1 p.Arg515Ter Pathogenic ★★ same condition
CTNNB1 p.Arg95Ter Pathogenic ★★ same condition
CTNNB1 p.Thr41Ala Likely pathogenic ★★ ⚠ same condition
CTNNB1 p.Val349fs Pathogenic ★★ same condition
CTNNB1 c.14-4A>G Benign/Likely benign ★★ same condition
CTNNB1 c.1683+17A>G Benign/Likely benign ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ctnnb1-p-val511fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown