Is CDHR1 p.Glu264fs (c.790del) pathogenic?

CDHR1 p.Glu264fs (c.790del) is classified Likely pathogenic in CDHR1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-09). Absent from gnomAD; Associated with CDHR1-related disorders.

What condition is associated with CDHR1 p.Glu264fs (c.790del)?

CDHR1 p.Glu264fs (c.790del) is associated with CDHR1-related disorders (ClinVar).

How common is CDHR1 p.Glu264fs (c.790del) in the general population?

CDHR1 p.Glu264fs (c.790del) is absent from gnomAD (gnomAD).

CDHR1 p.Glu264fs

c.790del · rs1842189258 · VCV866189

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

CDHR1-related disorders

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 9 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 4.8, 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: CDHR1
Protein: p.Glu264fs
Coding: c.790del
MANE Select: NM_033100
dbSNP: rs1842189258
Type: Deletion
Location: chr10:84204532 (GRCh38)
Gene constraint: LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.79
Residue 264: the cadherin 3 domain

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

Disease context

CDHR1-related disorders

Similar variants

CDHR1 p.Asp696fs Pathogenic ★★ same condition
CDHR1 p.Gly113fs Pathogenic ★★ same condition
CDHR1 p.Gly502fs Pathogenic ★★ same condition
CDHR1 p.His319fs Pathogenic ★★ same condition
CDHR1 p.Ile841fs Pathogenic/Likely pathogenic ★★ same condition
CDHR1 p.Thr86fs Pathogenic/Likely pathogenic ★★ same condition
CDHR1 p.Trp652fs Pathogenic/Likely pathogenic ★★ same condition
CDHR1 c.639+1del Likely 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/cdhr1-p-glu264fs (accessed [today's date]).

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