CDH9 p.Pro486=
c.1458G>A · rs35631322 · VCV791256
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.46%, 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 -11 | GERP -3.9 |
| Overall | ||
| CADD | 6.936 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.46%
African / African-American · 1,834/74,558 alleles
Filtering AF
2.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.33%
Overall
0.131%
2,097/1,603,438 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.46% | 41 |
| Remaining individualsnot grpmax-eligible | 0.163% | 615 |
| Admixed American | 0.117% | 851 |
| Middle Eastern | 0.0995% | 1,005 |
| South Asian | 0.0155% | 6,461 |
| East Asian | 0.00674% | 14,847 |
| European (non-Finnish) | 0.00589% | 16,981 |
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
- CDH9
- Protein
- p.Pro486=
- Coding
- c.1458G>A
- MANE Select
- NM_016279
- dbSNP
- rs35631322
- Type
- single nucleotide variant
- Location
- chr5:26889890 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 77.60
- Residue 486
- the cadherin 4 domain
Similar variants
- CDH9 p.Arg53Cys Uncertain significance ★★ ⚠ same type
- CDH9 p.Glu603Gly Benign ★★ ⚠ same type
- CDH9 p.Ala186Thr Uncertain significance ★ ⚠ same type
- CDH9 p.Ala412Ser Uncertain significance ★ ⚠ same type
- CDH9 p.Ala445Gly Uncertain significance ★ ⚠ same type
- CDH9 p.Ala500Glu Uncertain significance ★ ⚠ same type
- CDH9 p.Arg137Gln Uncertain significance ★ ⚠ same type
- CDH9 p.Arg519Gln Uncertain significance ★ ⚠ 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/cdh9-p-pro486 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown