CTNND2 p.Pro189=
c.567G>A · rs17802557 · VCV1280682
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 7.77%, nfe) — 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 -7.1 | GERP -4.2 |
| Overall | ||
| CADD | 1.031 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.77%
European (non-Finnish) · 91,646/1,180,006 alleles
Filtering AF
7.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.71%
Overall
6.67%
107,630/1,613,926 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 7.77% | 13 |
| Remaining individualsnot grpmax-eligible | 5.98% | 17 |
| Finnishnot grpmax-eligible | 5.91% | 17 |
| Ashkenazi Jewishnot grpmax-eligible | 5.65% | 18 |
| South Asian | 4.02% | 25 |
| Middle Eastern | 3.35% | 30 |
| Admixed American | 3.31% | 30 |
| African / African-American | 1.24% | 80 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| East Asian | 0.029% | 3,451 |
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.Pro189=
- Coding
- c.567G>A
- MANE Select
- NM_001332
- dbSNP
- rs17802557
- Type
- single nucleotide variant
- Location
- chr5:11397076 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.88
- Residue 189
- the 'disordered' region; a UniProt-annotated variant site (found in autism; likely pathogenic; hypomorphic variant affecting wnt signaling)
Similar variants
- CTNND2 p.Pro189Leu Likely benign ★ ⚠ same residue
- 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
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-pro189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown