Is CDH23 p.Glu901Lys (c.2701G>A) pathogenic?

CDH23 p.Glu901Lys (c.2701G>A) is classified Likely pathogenic in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-11-05). AlphaMissense: likely pathogenic (0.8724); Absent from gnomAD v4.1; Associated with Rare genetic deafness.

What condition is associated with CDH23 p.Glu901Lys (c.2701G>A)?

CDH23 p.Glu901Lys (c.2701G>A) is associated with Rare genetic deafness (ClinVar).

How common is CDH23 p.Glu901Lys (c.2701G>A) in the general population?

CDH23 p.Glu901Lys (c.2701G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDH23 p.Glu901Lys (c.2701G>A)?

AlphaMissense predicts likely pathogenic (score 0.8724) — an in-silico prediction, not a clinical call.

CDH23 p.Glu901Lys

c.2701G>A · rs876657636 · VCV228248

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8724 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, REVEL

Conditions

Rare genetic deafness

Computational evidence

Protein change
AlphaMissense	0.8724	likely pathogenic ✓ concordant with ClinVar
REVEL	0.859	moderately pathogenic-leaning
⇒ AlphaMissense and REVEL both call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.5	GERP 0.4, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 359 kb · p 0.017 · regional, not allelic
Overall
CADD	27.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Glu901Lys
Coding: c.2701G>A
MANE Select: NM_022124
dbSNP: rs876657636
Type: single nucleotide variant
Location: chr10:71702662 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 901: the cadherin 9 domain

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

Disease context

Rare genetic deafness — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDH23 c.6049+1G>A Pathogenic ★★ same condition
CDH23 c.7873-2A>T Pathogenic/Likely pathogenic ★★ same condition
CDH23 c.945+1G>T Pathogenic ★★ same condition
CDH23 p.Arg3186Ter Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Gly2017Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
CDH23 p.Thr1904= Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Tyr2927Ter Pathogenic ★★ same condition
CDH23 p.Arg702Trp Uncertain significance ★★ ⚠ same condition

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-glu901lys (accessed [today's date]).

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