CDH11 p.Gly301=
c.903C>T · rs55854547 · VCV2646591
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.18%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -0.29, phastCons 1 |
| Overall | ||
| CADD | 8.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.18%
Middle Eastern · 132/6,062 alleles
Filtering AF
1.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.76%
Overall
0.123%
1,988/1,613,590 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.18% | 46 |
| Amishnot grpmax-eligible | 1.86% | 54 |
| African / African-American | 0.549% | 182 |
| Ashkenazi Jewishnot grpmax-eligible | 0.463% | 216 |
| Admixed American | 0.357% | 280 |
| Remaining individualsnot grpmax-eligible | 0.227% | 440 |
| European (non-Finnish) | 0.0739% | 1,353 |
| South Asian | 0.0681% | 1,468 |
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.Gly301=
- Coding
- c.903C>T
- MANE Select
- NM_001797
- dbSNP
- rs55854547
- Type
- single nucleotide variant
- Location
- chr16:64988253 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.65
- Residue 301
- a UniProt-annotated variant site (in esws); the cadherin 3 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-gly301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown