Is CDH23 p.Ile2178= (c.6534C>T) pathogenic?

CDH23 p.Ile2178= (c.6534C>T) is classified Likely benign in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-04). Absent from gnomAD v4.1.

How common is CDH23 p.Ile2178= (c.6534C>T) in the general population?

CDH23 p.Ile2178= (c.6534C>T) is absent from gnomAD v4.1 (gnomAD).

CDH23 p.Ile2178=

c.6534C>T · rs1488349830 · VCV1104056

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.72	GERP -1.8, phastCons 1
Overall
CADD	7.144	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDH23
Protein: p.Ile2178=
Coding: c.6534C>T
MANE Select: NM_022124
dbSNP: rs1488349830
Type: single nucleotide variant
Location: chr10:71793462 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2178: the cadherin 21 domain

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

Similar variants

CDH23 p.Ile2178Phe Uncertain significance ★★ ⚠ same residue
CDH23 p.Ile2178Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH23 p.Arg2029Trp Pathogenic ★★★ ⚠ same type
CDH23 p.Asp127Gly Likely pathogenic ★★★ same type
CDH23 p.Glu956Lys Pathogenic ★★★ same type
CDH23 p.Pro240Leu Pathogenic ★★★ same type
CDH23 c.1515-12G>A Uncertain significance ★★★ same type
CDH23 p.Ala3190Val Uncertain significance ★★★ ⚠ 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-ile2178 (accessed [today's date]).

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