CDH9 p.Gln274=
c.822A>G · rs373715996 · VCV2655377
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0334%, mid)
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 -5.9 | GERP -4.4 |
| Overall | ||
| CADD | 0.614 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0334%
Middle Eastern · 2/5,988 alleles
Filtering AF
0.00729%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0068%
Overall
0.00752%
117/1,555,930 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0334% | 2,994 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,640 |
| European (non-Finnish) | 0.00874% | 11,448 |
| East Asian | 0.00451% | 22,194 |
| South Asian | 0.00363% | 27,550 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00351% | 28,508 |
| Finnishnot grpmax-eligible | 0.00157% | 63,802 |
| African / African-American | 0.00138% | 72,582 |
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.Gln274=
- Coding
- c.822A>G
- MANE Select
- NM_016279
- dbSNP
- rs373715996
- Type
- single nucleotide variant
- Location
- chr5:26903814 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 77.60
- Residue 274
- the cadherin 3 domain
Similar variants
- CDH9 p.Arg53Cys Uncertain significance ★★ ⚠ same type
- CDH9 p.Glu603Gly Benign ★★ ⚠ same type
- CDH9 p.Pro486= 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
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-gln274 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown