Is CDH23 p.Arg3026= (c.9078G>C) pathogenic?

CDH23 p.Arg3026= (c.9078G>C) is classified Conflicting classifications of pathogenicity in CDH23 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-24). Ultra-rare (popmax 0.0164%, mid); Associated with Inborn genetic diseases.

What condition is associated with CDH23 p.Arg3026= (c.9078G>C)?

CDH23 p.Arg3026= (c.9078G>C) is associated with Inborn genetic diseases, Usher syndrome type 1 (ClinVar).

How common is CDH23 p.Arg3026= (c.9078G>C) in the general population?

CDH23 p.Arg3026= (c.9078G>C) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

CDH23 p.Arg3026=

c.9078G>C · rs727504725 · VCV179230

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>A here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.6	GERP 0.62, phastCons 1
Overall
CADD	13.8	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,082 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00062% 10/1,613,648 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,082
African / African-American	0.00534%	18,711
Remaining individualsnot grpmax-eligible	0.0032%	31,232
Admixed American	0.00167%	59,990
European (non-Finnish)	0.00017%	589,922

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.Arg3026=
Coding: c.9078G>C
MANE Select: NM_022124
dbSNP: rs727504725
Type: single nucleotide variant
Location: chr10:71811315 (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

Also linked: Usher syndrome type 1

Similar variants

CDH23 p.Arg3026Gln Uncertain significance ★★ ⚠ same residue
CDH23 p.Arg3026Trp Uncertain significance ★ 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

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-arg3026 (accessed [today's date]).

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