Is CDHR1 p.Val469fs (c.1405del) pathogenic?

CDHR1 p.Val469fs (c.1405del) is classified Pathogenic in CDHR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-23). Absent from gnomAD.

How common is CDHR1 p.Val469fs (c.1405del) in the general population?

CDHR1 p.Val469fs (c.1405del) is absent from gnomAD (gnomAD).

CDHR1 p.Val469fs

c.1405del · rs2492531858 · VCV2092326

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 13 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.67	GERP -2, phastCons 0.032

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: CDHR1
Protein: p.Val469fs
Coding: c.1405del
MANE Select: NM_033100
dbSNP: rs2492531858
Type: Deletion
Location: chr10:84211085 (GRCh38)
Gene constraint: LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.79
Residue 469: the cadherin 4 domain

Full CDHR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDHR1 p.Asp238fs Pathogenic/Likely pathogenic ★★ same type
CDHR1 p.Asp696fs Pathogenic ★★ same type
CDHR1 p.Cys4fs Likely pathogenic ★★ same type
CDHR1 p.Glu264fs Likely pathogenic ★★ same type
CDHR1 p.Glu99fs Pathogenic ★★ same type
CDHR1 p.Gly113fs Pathogenic ★★ same type
CDHR1 p.Gly488fs Pathogenic ★★ same type
CDHR1 p.Gly502fs Pathogenic ★★ 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/cdhr1-p-val469fs (accessed [today's date]).

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