Is CDH23 p.Cys9Phe (c.26G>T) pathogenic?

CDH23 p.Cys9Phe (c.26G>T) is classified Uncertain significance in CDH23 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-01-16). AlphaMissense: likely benign (0.0535); Very rare (popmax 0.000864%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CDH23 p.Cys9Phe (c.26G>T)?

CDH23 p.Cys9Phe (c.26G>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDH23 p.Cys9Phe (c.26G>T) in the general population?

CDH23 p.Cys9Phe (c.26G>T) is very rare (popmax 0.000864%, nfe) (gnomAD).

What do computational predictors say about CDH23 p.Cys9Phe (c.26G>T)?

AlphaMissense predicts likely benign (score 0.0535) — an in-silico prediction, not a clinical call.

CDH23 p.Cys9Phe

c.26G>T · rs2132005093 · VCV1907491

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0535 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000864%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0535	likely benign
REVEL	0.03	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP -1.4, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 359 kb · p 0.017 · regional, not allelic
Overall
CADD	15.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000864% European (non-Finnish) · 10/1,158,042 alleles

Filtering AF 0.000437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000318%

Overall 0.000704% 10/1,420,710 alleles · very rare

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.Cys9Phe
Coding: c.26G>T
MANE Select: NM_022124
dbSNP: rs2132005093
Type: single nucleotide variant
Location: chr10:71439857 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

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

Disease context

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

Similar variants

CDH23 p.Cys9= Likely benign ★ same residue
CDH23 p.Ala129Thr Uncertain significance ★★ ⚠ same condition
CDH23 p.Ala1464Glu Uncertain significance ★★ ⚠ same condition
CDH23 p.Ala1482Val Uncertain significance ★★ ⚠ same condition
CDH23 p.Ala1673Val Uncertain significance ★★ same condition
CDH23 p.Ala1878Thr Uncertain significance ★★ same condition
CDH23 p.Ala1974Thr Uncertain significance ★★ ⚠ same condition
CDH23 p.Ala1987Thr 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-cys9phe (accessed [today's date]).

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