CTNND2 p.Ala3=
c.9G>C · rs1232627080 · VCV2655300
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00293%, afr)
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 -0.11 | GERP -1.4, phastCons 0.17 |
| Overall | ||
| CADD | 7.835 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00293%
African / African-American · 2/68,210 alleles
Filtering AF
0.00128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0011%
Overall
0.00162%
24/1,483,800 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00293% | 34,105 |
| European (non-Finnish) | 0.00196% | 51,053 |
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
- CTNND2
- Protein
- p.Ala3=
- Coding
- c.9G>C
- MANE Select
- NM_001332
- dbSNP
- rs1232627080
- Type
- single nucleotide variant
- Location
- chr5:11903845 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.88
- Residue 3
- the 'disordered' region
Similar variants
- CTNND2 p.Asp700Gly Uncertain significance ★★ ⚠ same type
- CTNND2 p.Asp802Asn Uncertain significance ★★ ⚠ same type
- CTNND2 p.Glu217Asp Uncertain significance ★★ ⚠ same type
- CTNND2 c.1178-153T>C Likely benign ★★ same type
- CTNND2 c.1178-164G>A Benign ★★ same type
- CTNND2 c.1372+105T>C Likely benign ★★ same type
- CTNND2 c.1628+51C>T Benign ★★ same type
- CTNND2 c.174+104C>T Benign ★★ 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/ctnnd2-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown