Is CRX p.Arg41del (c.118CGG[1]) pathogenic?

CRX p.Arg41del (c.118CGG[1]) is classified Likely pathogenic in CRX (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-19). Associated with CRX-related disorders.

What condition is associated with CRX p.Arg41del (c.118CGG[1])?

CRX p.Arg41del (c.118CGG[1]) is associated with CRX-related disorders (ClinVar).

CRX p.Arg41del

c.118CGG[1] · VCV4943124

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

CRX-related disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 10	GERP 0.73, phastCons 1

Variant & gene context

Gene: CRX
Protein: p.Arg41del
Coding: c.118CGG[1]
MANE Select: NM_000554
Type: Microsatellite
Location: chr19:47836259 (GRCh38)
Gene constraint: LOEUF 0.673 · pLI 0.72 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 61.78 · 1 PDB
Residue 41: a DNA-binding region; a UniProt-annotated variant site (in rp); a UniProt-annotated variant site (in cord2; exhibits reduced dna binding, transcriptional synergy and interaction with nrl)

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

Disease context

CRX-related disorders

Similar variants

CRX p.Arg41Gln Pathogenic/Likely pathogenic ★★ same residue
CRX p.Arg41Pro Likely pathogenic ★★ same residue
CRX p.Leu179fs Pathogenic/Likely pathogenic ★★ same condition
CRX p.Arg41= Likely benign ★★ same residue
CRX p.Ser203fs Pathogenic ★ same condition
CRX p.Arg41Trp Pathogenic same residue
CRX c.100+3_100+5delinsTTA Pathogenic/Likely pathogenic ★★ same condition
CRX p.Ala166_Ser167insTer Pathogenic/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/crx-p-arg41del (accessed [today's date]).

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