Is CDH23 p.Arg3096fs (c.9284dup) pathogenic?

CDH23 p.Arg3096fs (c.9284dup) is classified Pathogenic/Likely pathogenic in CDH23 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2023-09-16). Absent from gnomAD; Associated with CDH23-related disorder.

What condition is associated with CDH23 p.Arg3096fs (c.9284dup)?

CDH23 p.Arg3096fs (c.9284dup) is associated with CDH23-related disorder, Usher syndrome type 1, pituitary adenoma 5, multiple types (ClinVar).

How common is CDH23 p.Arg3096fs (c.9284dup) in the general population?

CDH23 p.Arg3096fs (c.9284dup) is absent from gnomAD (gnomAD).

CDH23 p.Arg3096fs

c.9284dup · rs1564808024 · VCV623742

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

CDH23-related disorder

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 65 of 70
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP 0.56, 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.Arg3096fs
Coding: c.9284dup
MANE Select: NM_022124
dbSNP: rs1564808024
Type: Duplication
Location: chr10:71811716 (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

CDH23-related disorder

Also linked: Usher syndrome type 1 pituitary adenoma 5, multiple types

Similar variants

CDH23 p.Glu1753Ter Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Gly2783fs Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.His1769fs Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Thr188fs Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Thr477fs Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Arg140fs Likely pathogenic ★ same condition
CDH23 p.Asp1491fs Likely pathogenic ★ same condition
CDH23 p.Glu703fs 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-arg3096fs (accessed [today's date]).

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