CTNNB1 p.Arg515=
c.1543C>A · rs397514554 · VCV2752873
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 11.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,074 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000342%
5/1,461,888 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,769 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CTNNB1
- Protein
- p.Arg515=
- Coding
- c.1543C>A
- MANE Select
- NM_001904
- dbSNP
- rs397514554
- Type
- single nucleotide variant
- Location
- chr3:41234157 (GRCh38)
- Gene constraint
- LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02 · 50 PDB
- Residue 515
- an α-helix
Similar variants
- CTNNB1 p.Arg515Ter Pathogenic ★★ same residue
- CTNNB1 p.Arg515Gln Uncertain significance ★ same residue
- CTNNB1 c.1081+1G>T Pathogenic/Likely pathogenic ★★ same type
- CTNNB1 c.1082-1G>C Pathogenic ★★ same type
- CTNNB1 c.735-1G>C Pathogenic ★★ same type
- CTNNB1 p.Arg474Ter Pathogenic ★★ same type
- CTNNB1 p.Arg535Ter Pathogenic ★★ same type
- CTNNB1 p.Arg587Ter Pathogenic/Likely pathogenic ★★ same type
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-arg515 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown