Is CDH23 p.Val1800= (c.5400G>A) pathogenic?

CDH23 p.Val1800= (c.5400G>A) is classified Likely benign in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-30). Very rare (popmax 8.48e-05%, nfe).

How common is CDH23 p.Val1800= (c.5400G>A) in the general population?

CDH23 p.Val1800= (c.5400G>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

CDH23 p.Val1800=

c.5400G>A · VCV4907889

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

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 2.6	GERP 0.8, phastCons 1
Overall
CADD	6.386	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,818 alleles

Overall 6.2e-05% 1/1,613,914 alleles · very rare exomes 1/1,461,576 · genomes 0/152,338 · joint denominator

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.Val1800=
Coding: c.5400G>A
MANE Select: NM_022124
Type: single nucleotide variant
Location: chr10:71784318 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1800: the cadherin 17 domain

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

Similar variants

CDH23 p.Val1800Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH23 p.Val1800Leu Uncertain significance ★ ⚠ same residue
CDH23 p.Val1800Met Uncertain significance ★ ⚠ 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

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-val1800 (accessed [today's date]).

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