CDH11 p.Ser315=
c.945G>A · rs28216 · VCV1192581
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 42.9%, nfe) — too common for a highly-penetrant pathogenic allele
Conditions
1
Elsahy-Waters syndrome
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 1.1 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 14.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
42.9%
European (non-Finnish) · 505,430/1,178,466 alleles
Filtering AF
42.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 42.7%
Overall
38.6%
621,678/1,611,772 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 42.9% | 2 |
| Amishnot grpmax-eligible | 41.3% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 39.2% | 3 |
| Remaining individualsnot grpmax-eligible | 37.5% | 3 |
| Middle Eastern | 35.4% | 3 |
| Finnishnot grpmax-eligible | 34.1% | 3 |
| South Asian | 26.5% | 4 |
| Admixed American | 24.2% | 4 |
| East Asian | 20.9% | 5 |
| African / African-American | 12% | 8 |
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
- CDH11
- Protein
- p.Ser315=
- Coding
- c.945G>A
- MANE Select
- NM_001797
- dbSNP
- rs28216
- Type
- single nucleotide variant
- Location
- chr16:64988211 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.65
- Residue 315
- a UniProt-annotated variant site (in esws); the cadherin 3 domain
Similar variants
- CDH11 p.Asp260Asn Pathogenic/Likely pathogenic ★★ same condition
- CDH11 c.1253+43G>C Benign ★★ same condition
- CDH11 c.1642+20C>T Benign ★★ same condition
- CDH11 c.644-11T>C Benign ★★ same condition
- CDH11 c.811+13A>G Benign ★★ same condition
- CDH11 p.Met275Ile Benign ★★ ⚠ same condition
- CDH11 p.Ser373Ala Benign ★★ same condition
- CDH11 p.Thr255Met Benign ★★ ⚠ same condition
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/cdh11-p-ser315 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown