Is CDH23 p.Phe671fs (c.2012del) pathogenic?

CDH23 p.Phe671fs (c.2012del) is classified Pathogenic in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2010-10-06). Absent from gnomAD; Associated with Rare genetic deafness.

What condition is associated with CDH23 p.Phe671fs (c.2012del)?

CDH23 p.Phe671fs (c.2012del) is associated with Rare genetic deafness (ClinVar).

How common is CDH23 p.Phe671fs (c.2012del) in the general population?

CDH23 p.Phe671fs (c.2012del) is absent from gnomAD (gnomAD).

CDH23 p.Phe671fs

c.2012del · rs397517313 · VCV45886

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

Conditions

Rare genetic deafness

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 19 of 70
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP -0.72, 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.Phe671fs
Coding: c.2012del
MANE Select: NM_022124
dbSNP: rs397517313
Type: Deletion
Location: chr10:71687671 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 671: the cadherin 6 domain; a β-strand

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 p.Glu2138fs Likely pathogenic ★ same condition
CDH23 p.Val16fs Pathogenic ★ same condition
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

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-phe671fs (accessed [today's date]).

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