Is CDH23 p.Phe67fs (c.201del) pathogenic?

CDH23 p.Phe67fs (c.201del) is classified Pathogenic in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-25). Absent from gnomAD.

How common is CDH23 p.Phe67fs (c.201del) in the general population?

CDH23 p.Phe67fs (c.201del) is absent from gnomAD (gnomAD).

CDH23 p.Phe67fs

c.201del · rs2493189700 · VCV3007906

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 70
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.2	GERP 0.59, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDH23
Protein: p.Phe67fs
Coding: c.201del
MANE Select: NM_022124
dbSNP: rs2493189700
Type: Deletion
Location: chr10:71510135 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 67: the cadherin 1 domain

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

Similar variants

CDH23 p.Phe67Cys Uncertain significance ★ same residue
CDH23 p.Phe67= Likely benign ★ same residue
CDH23 c.1143_1176del Pathogenic/Likely pathogenic ★★ same type
CDH23 c.336+1del Likely pathogenic ★★ same type
CDH23 c.9280_9286del Pathogenic/Likely pathogenic ★★ same type
CDH23 p.Ala2232_Val2233insTer Pathogenic/Likely pathogenic ★★ same type
CDH23 p.Ala2309fs Pathogenic/Likely pathogenic ★★ same type
CDH23 p.Ala2685fs 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-phe67fs (accessed [today's date]).

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