CDH13 p.Gln288=
c.864G>A · rs35282700 · VCV778616
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.93%, 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 2.8 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 7.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.93%
African / African-American · 2,202/75,032 alleles
Filtering AF
2.83%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.79%
Overall
0.177%
2,852/1,613,952 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.93% | 34 |
| Admixed American | 0.25% | 400 |
| Remaining individualsnot grpmax-eligible | 0.237% | 422 |
| Middle Eastern | 0.198% | 505 |
| European (non-Finnish) | 0.0279% | 3,586 |
| South Asian | 0.011% | 9,109 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- CDH13
- Protein
- p.Gln288=
- Coding
- c.864G>A
- MANE Select
- NM_001257
- dbSNP
- rs35282700
- Type
- single nucleotide variant
- Location
- chr16:83486559 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.19 · 1 PDB
- Residue 288
- the cadherin 2 domain
Similar variants
- CDH13 p.Gln288Arg Uncertain significance ★ ⚠ same residue
- CDH13 c.1102-6T>C Benign ★★ same type
- CDH13 c.1284+90A>G Benign ★★ same type
- CDH13 c.1539-109T>C Benign ★★ same type
- CDH13 c.1681+64T>C Benign ★★ same type
- CDH13 c.1682-151C>T Benign ★★ same type
- CDH13 c.1682-180G>A Benign ★★ same type
- CDH13 c.1682-59A>G 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/cdh13-p-gln288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown