CDH11 p.Ala711=
c.2133G>A · rs200766127 · VCV2646587
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.467%, sas)
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 -5.5 | GERP -4.9 |
| Overall | ||
| CADD | 0.836 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.467%
South Asian · 425/91,078 alleles
Filtering AF
0.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.416%
Overall
0.0433%
699/1,614,100 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.467% | 214 |
| Middle Eastern | 0.132% | 758 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,977 |
| Finnishnot grpmax-eligible | 0.0203% | 4,925 |
| European (non-Finnish) | 0.0192% | 5,221 |
| Admixed American | 0.00666% | 15,004 |
| African / African-American | 0.00267% | 37,509 |
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.Ala711=
- Coding
- c.2133G>A
- MANE Select
- NM_001797
- dbSNP
- rs200766127
- Type
- single nucleotide variant
- Location
- chr16:64947861 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.65
- Residue 711
- a UniProt-annotated variant site (in esws)
Similar variants
- CDH11 p.Asp260Asn Pathogenic/Likely pathogenic ★★ same type
- CDH11 p.Ala228Ser Uncertain significance ★★ ⚠ same type
- CDH11 p.Arg556Trp Uncertain significance ★★ ⚠ same type
- CDH11 p.Asp718Asn Uncertain significance ★★ ⚠ same type
- CDH11 p.Gly45Arg Uncertain significance ★★ ⚠ same type
- CDH11 p.Gly618Ser Uncertain significance ★★ ⚠ same type
- CDH11 p.Ile649Val Uncertain significance ★★ ⚠ same type
- CDH11 c.1253+43G>C 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/cdh11-p-ala711 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown