CDH23 p.Asp2936=
c.8808C>T · rs148743086 · VCV46054
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.869%, afr)
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 2.2 | GERP -0.63, phastCons 1 |
| Overall | ||
| CADD | 8.797 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.869%
African / African-American · 652/75,064 alleles
Filtering AF
0.813%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.791%
Overall
0.0444%
717/1,613,288 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.869% | 115 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Admixed American | 0.045% | 2,223 |
| South Asian | 0.0022% | 45,544 |
| European (non-Finnish) | 0.000509% | 196,649 |
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.Asp2936=
- Coding
- c.8808C>T
- MANE Select
- NM_022124
- dbSNP
- rs148743086
- Type
- single nucleotide variant
- Location
- chr10:71809905 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2936
- the cadherin 27 domain
Similar variants
- 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
- CDH23 p.Arg3189Gln 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-asp2936 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown