CDH11 p.Ala9=
c.27C>T · VCV3998800
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0362%, eas)
Conditions
1
Inborn genetic diseases
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 -4.1 |
| Overall | ||
| CADD | 6.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0362%
East Asian · 15/41,484 alleles
Filtering AF
0.0222%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.00257%
40/1,558,600 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0362% | 2,766 |
| Remaining individualsnot grpmax-eligible | 0.00663% | 15,078 |
| South Asian | 0.00354% | 28,283 |
| African / African-American | 0.00273% | 36,687 |
| European (non-Finnish) | 0.00139% | 71,960 |
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.Ala9=
- Coding
- c.27C>T
- MANE Select
- NM_001797
- Type
- single nucleotide variant
- Location
- chr16:65004843 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.65
Similar variants
- CDH11 p.Ala228Ser Uncertain significance ★★ ⚠ same condition
- CDH11 p.Arg556Trp Uncertain significance ★★ ⚠ same condition
- CDH11 p.Gly45Arg Uncertain significance ★★ ⚠ same condition
- CDH11 p.Gly618Ser Uncertain significance ★★ ⚠ same condition
- CDH11 p.Ile649Val Uncertain significance ★★ ⚠ same condition
- CDH11 p.Val478Ile Likely benign ★★ same condition
- CDH11 p.Ala470Val Uncertain significance ★ ⚠ same condition
- CDH11 p.Ala475Thr Uncertain significance ★ ⚠ 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-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown