CDH11 p.Pro157=
c.471G>A · VCV3898181
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.052%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.094 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -4.7 |
| Overall | ||
| CADD | 7.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.052%
African / African-American · 39/74,990 alleles
Filtering AF
0.039%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0345%
Overall
0.0044%
71/1,614,038 alleles · ultra-rare
exomes 43/1,461,888 · genomes 28/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.052% | 1,923 |
| East Asian | 0.00892% | 11,208 |
| South Asian | 0.00439% | 22,766 |
| Admixed American | 0.00333% | 30,007 |
| European (non-Finnish) | 0.00178% | 56,192 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
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.Pro157=
- Coding
- c.471G>A
- MANE Select
- NM_001797
- Type
- single nucleotide variant
- Location
- chr16:64998614 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.65
- Residue 157
- the cadherin 1 domain
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-pro157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown