GENE REFERENCE / HGNC:2383

CRX

cone-rod homeobox

protein-coding gene19q13.33Gene information

What does this gene do?

The CRX gene provides instructions for making a protein called the cone-rod homeobox protein. This protein is found in the eyes, specifically in the light-sensitive tissue at the back of the eye called the retina. The cone-rod homeobox protein attaches (binds) to specific regions of DNA and helps control the activity of particular genes. On the basis of this action, this protein is called a transcription factor.

In the retina, the cone-rod homeobox protein is necessary for the normal development of light-detecting cells called photoreceptors. Through its actions as a transcription factor, the cone-rod homeobox protein helps photoreceptor cells mature into two types: rods and cones. Rods are needed for vision in low light, while cones are needed for vision in bright light, including color vision. The protein also helps maintain these cells and preserve vision.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2016-02.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
cone-rod dystrophy 2MONDO:0007362 · Evaluated 2024-12-06	Autosomal dominant	DefinitiveRetina Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 658
Submissions for variants in or overlapping this gene: 1,331
Submissions explicitly reporting this gene: 1,241
Alleles reported pathogenic / likely pathogenic: 166
VariationIDs with uncertain significance: 267
VariationIDs with conflicting classifications: 42

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about CRX?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 166 alleles in CRX reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in CRX.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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