Is CDH23 p.Ala1464= (c.4392G>C) pathogenic?

CDH23 p.Ala1464= (c.4392G>C) is classified Likely benign in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-02-11). Absent from gnomAD v4.1.

How common is CDH23 p.Ala1464= (c.4392G>C) in the general population?

CDH23 p.Ala1464= (c.4392G>C) is absent from gnomAD v4.1 (gnomAD).

CDH23 p.Ala1464=

c.4392G>C · rs770421619 · VCV1531980

Likely benign Single submitter

Classification

Likely benign

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 carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -9.8	GERP -5.3
Overall
CADD	0.025	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.Ala1464=
Coding: c.4392G>C
MANE Select: NM_022124
dbSNP: rs770421619
Type: single nucleotide variant
Location: chr10:71739676 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1464: the cadherin 14 domain; an α-helix

Full CDH23 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDH23 p.Ala1464Glu Uncertain significance ★★ ⚠ same residue
CDH23 p.Ala1464Thr Uncertain significance ★★ ⚠ same residue
CDH23 p.Ala1464Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH23 p.Ala1464Val Conflicting classifications of pathogenicity ★ ⚠ 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

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-ala1464 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown