CDH23 p.Arg2029=
c.6085C>A · rs750880909 · VCV1412409
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.92 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.61 | gain · loss 0.31 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 0.71, phastCons 1 |
| Overall | ||
| CADD | 22.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDH23
- Protein
- p.Arg2029=
- Coding
- c.6085C>A
- MANE Select
- NM_022124
- dbSNP
- rs750880909
- Type
- single nucleotide variant
- Location
- chr10:71791167 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2029
- a UniProt-annotated variant site (in dfnb12); the cadherin 19 domain
Similar variants
- CDH23 p.Arg2029Trp Pathogenic ★★★ ⚠ same residue
- CDH23 p.Arg2029Gln Uncertain significance ★★ ⚠ same residue
- 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-arg2029 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown