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Gene

CRX

cone-rod homeobox

Summary

Cytogenetic location
19q13.33
Coordinates
Chromosome 19: 47,821,937–47,843,324 (GRCh38)
Exons
4 exons across 21.4 kb
Protein
299 amino acids
Inheritance
Autosomal recessive
Also known as
CRD, LCA7, OTX3
Previous symbols
CORD2
MANE Select transcript
ENST00000221996.12NM_000554.6
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Leber Congenital Amaurosis & RPE65-Related Retinopathy

    • Leber Congenital AmaurosisAutosomal recessive

      A group of inherited retinal dystrophies, caused by changes in genes such as CEP290, GUCY2D, CRB1, RPE65 and AIPL1, that cause severe vision loss, nystagmus and poor pupil responses in infancy.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Confirming the gene can determine eligibility for gene-specific treatments and clinical trials, and informs family counselling.

Broader groupings

  • Retinitis Pigmentosa

    • One of 77 genes linked to it

      A group of inherited retinal dystrophies with progressive loss of rod and then cone photoreceptors, causing night blindness and gradual loss of peripheral vision.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CRX is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where CRX sits. CRX and 25 genes near it on chromosome 19, from 47,332,631 to 48,332,630.Chromosome 1919q13.33p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4347.4 Mb47.6 Mb47.8 Mb48 Mb48.2 MbC5AR2: 47,332,148–47,347,329, forward strandC5AR2DHX34: 47,349,280–47,383,255, forward strandDHX34MEIS3: 47,403,117–47,419,530, reverse strandMEIS3SLC8A2: 47,428,017–47,472,184, reverse strandSLC8A2KPTN: 47,475,141–47,484,265, reverse strandKPTNNAPA: 47,484,530–47,515,122, reverse strandNAPAZNF541: 47,520,638–47,573,148, reverse strandZNF541BICRA: 47,608,196–47,703,277, forward strandBICRAEHD2: 47,713,388–47,745,089, forward strandEHD2NOP53: 47,745,481–47,758,208, forward strandNOP53SELENOW: 47,778,508–47,784,686, forward strandSELENOWTPRX1: 47,801,232–47,819,051, reverse strandTPRX1CRX: 47,821,937–47,843,324, forward strandCRXTPRX2: 47,859,235–47,861,721, forward strandTPRX2SULT2A1: 47,870,327–47,886,479, reverse strandSULT2A1BSPH1: 47,968,046–47,992,170, reverse strandBSPH1ELSPBP1: 47,994,632–48,025,154, forward strandELSPBP1CABP5: 48,029,383–48,044,079, reverse strandCABP5PLA2G4C: 48,047,843–48,111,390, reverse strandPLA2G4CLIG1: 48,115,444–48,170,654, reverse strandLIG1ZSWIM9: 48,170,645–48,197,624, forward strandZSWIM9CARD8: 48,180,770–48,255,976, reverse strandCARD8ZNF114: 48,270,041–48,289,292, forward strandZNF114ODAD1: 48,296,355–48,321,971, reverse strandODAD1EMP3: 48,321,310–48,330,560, forward strandEMP3TMEM143: 48,329,918–48,364,245, reverse strandTMEM143Diagram of CRX: 4 exons on the forward strand of chromosome 19Exon 2: 2 known disease-causing sitesExon 3: 18 known disease-causing sitesExon 4: 70 known disease-causing sitesExon 1: 47,821,937–47,822,010, 74 basesExon 2: 47,834,409–47,834,543, 135 basesExon 3: 47,836,243–47,836,394, 152 basesExon 4: 47,839,320–47,843,324, 4,005 bases12345′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 4.4 kb of the gene's 21.4 kb; 900 of those bases code for the protein.

How a genome test reads CRX

94

positions in CRX where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 21.4 kb of CRX, introns included, not only the 4.4 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). CRX gene: cone-rod homeobox. Retrieved 17 October 2026, from https://dantelabs.com/genes/crx

Vancouver

Dante Labs. CRX gene: cone-rod homeobox [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/crx

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