CDH23 p.Phe2891=
c.8673C>T · rs767574624 · VCV799971
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00172%, amr)
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 3.3 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 9.678 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00172%
Admixed American · 1/58,178 alleles
Filtering AF
0.000882%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000721%
Overall
0.00112%
18/1,600,708 alleles · very rare
exomes 16/1,448,434 · genomes 2/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00172% | 58,178 |
| European (non-Finnish) | 0.00145% | 69,027 |
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
- CDH23
- Protein
- p.Phe2891=
- Coding
- c.8673C>T
- MANE Select
- NM_022124
- dbSNP
- rs767574624
- Type
- single nucleotide variant
- Location
- chr10:71807958 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2891
- the cadherin 27 domain
Similar variants
- CDH23 p.Phe2891Cys Uncertain significance ★ ⚠ same residue
- CDH23 p.Arg2029Trp Pathogenic ★★★ ⚠ same type
- CDH23 p.Asp127Gly Likely pathogenic ★★★ same type
- CDH23 p.Glu956Lys Pathogenic ★★★ same type
- CDH23 p.Pro240Leu Pathogenic ★★★ same type
- CDH23 c.1515-12G>A Uncertain significance ★★★ same type
- CDH23 p.Ala3190Val Uncertain significance ★★★ same type
- CDH23 p.Arg301Gln Uncertain significance ★★★ 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/cdh23-p-phe2891 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown