Is CDH23 p.Arg736Gln (c.2207G>A) pathogenic?

CDH23 p.Arg736Gln (c.2207G>A) is classified Uncertain significance in CDH23 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-09-01). AlphaMissense: ambiguous (0.4918); Ultra-rare (popmax 0.0185%, nfe); Associated with Usher syndrome type 1.

What condition is associated with CDH23 p.Arg736Gln (c.2207G>A)?

CDH23 p.Arg736Gln (c.2207G>A) is associated with Usher syndrome type 1 (ClinVar).

How common is CDH23 p.Arg736Gln (c.2207G>A) in the general population?

CDH23 p.Arg736Gln (c.2207G>A) is ultra-rare (popmax 0.0185%, nfe) (gnomAD).

How is Usher syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about CDH23 p.Arg736Gln (c.2207G>A)?

AlphaMissense predicts ambiguous (score 0.4918) — an in-silico prediction, not a clinical call.

CDH23 p.Arg736Gln

c.2207G>A · rs377348311 · VCV850599

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

ambiguous

0.4918 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0185%, nfe)

Conditions

Usher syndrome type 1

Computational evidence

Protein change
AlphaMissense	0.4918	ambiguous
REVEL	0.786	moderately pathogenic-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 359 kb · p 0.017 · regional, not allelic
Overall
CADD	33.0	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

Grpmax group 0.0185% European (non-Finnish) · 218/1,179,834 alleles

Filtering AF 0.0165% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0157%

Overall 0.0148% 238/1,613,532 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0185%	5,412
Remaining individualsnot grpmax-eligible	0.0176%	5,678
African / African-American	0.0107%	9,355
South Asian	0.0011%	91,066

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.Arg736Gln
Coding: c.2207G>A
MANE Select: NM_022124
dbSNP: rs377348311
Type: single nucleotide variant
Location: chr10:71694177 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 736: the cadherin 7 domain; a turn

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

Disease context

Usher syndrome type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Usher syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

CDH23 p.Arg736Ter Pathogenic ★★ same residue
CDH23 p.Arg2029Trp Pathogenic ★★★ ⚠ same condition
CDH23 p.Asp127Gly Likely pathogenic ★★★ same condition
CDH23 p.Glu956Lys Pathogenic ★★★ same condition
CDH23 p.Pro240Leu Pathogenic ★★★ same condition
CDH23 c.1515-12G>A Uncertain significance ★★★ same condition
CDH23 p.Arg301Gln Uncertain significance ★★★ same condition
CDH23 p.Arg3189Gln 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-arg736gln (accessed [today's date]).

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