Is CDH23 p.Ile2420fs (c.7258del) pathogenic?

CDH23 p.Ile2420fs (c.7258del) is classified Likely pathogenic in CDH23 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-20). Absent from gnomAD; Associated with pituitary adenoma 5, multiple types.

What condition is associated with CDH23 p.Ile2420fs (c.7258del)?

CDH23 p.Ile2420fs (c.7258del) is associated with pituitary adenoma 5, multiple types (ClinVar).

How common is CDH23 p.Ile2420fs (c.7258del) in the general population?

CDH23 p.Ile2420fs (c.7258del) is absent from gnomAD (gnomAD).

How is Familial isolated pituitary adenoma inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

CDH23 p.Ile2420fs

c.7258del · rs2494405112 · VCV2680490

Likely pathogenic Single submitter

Classification

Likely 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

pituitary adenoma 5, multiple types

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 52 of 70
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 1.9, 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.Ile2420fs
Coding: c.7258del
MANE Select: NM_022124
dbSNP: rs2494405112
Type: Deletion
Location: chr10:71799524 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2420: the cadherin 23 domain

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

Disease context

pituitary adenoma 5, multiple types — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial isolated pituitary adenoma (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood, Elderly, Infancy

Similar variants

CDH23 c.1143_1176del Pathogenic/Likely pathogenic ★★ same condition
CDH23 c.9280_9286del Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Ala2232_Val2233insTer Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Ala2685fs Pathogenic ★★ same condition
CDH23 p.Arg2115fs Pathogenic/Likely pathogenic ★★ same condition
CDH23 p.Asn1889fs Likely pathogenic ★★ same condition
CDH23 p.Asp2716fs Likely pathogenic ★★ same condition
CDH23 p.Ile2132fs 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-ile2420fs (accessed [today's date]).

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