Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 12.5%, amr) — too common for a highly-penetrant pathogenic allele
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 7.5 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 11.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
12.5%
Admixed American · 7,472/59,892 alleles
Filtering AF
12.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.1%
Overall
0.879%
14,190/1,613,700 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 12.5% | 8 |
| East Asian | 11.3% | 9 |
| Remaining individualsnot grpmax-eligible | 1.3% | 77 |
| South Asian | 0.359% | 278 |
| African / African-American | 0.291% | 344 |
| Middle Eastern | 0.0495% | 2,020 |
| European (non-Finnish) | 0.0256% | 3,907 |
| Finnishnot grpmax-eligible | 0.0109% | 9,139 |
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.Asp780=
- Coding
- c.2340C>T
- MANE Select
- NM_001904
- dbSNP
- rs2293303
- Type
- single nucleotide variant
- Location
- chr3:41239336 (GRCh38)
- Gene constraint
- LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02 · 50 PDB
- Residue 780
- a β-strand; the 'disordered' region; the 'interaction with scrib' region; a UniProt-annotated variant site (in nedsdv; the patient also manifest features of exudative vitreoretinopathy)
Similar variants
- 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.Arg515Ter Pathogenic ★★ same type
- CTNNB1 p.Arg535Ter Pathogenic ★★ same type
- CTNNB1 p.Arg587Ter Pathogenic/Likely pathogenic ★★ same type
- CTNNB1 p.Arg661Ter 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-asp780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown