CRX cone-rod homeobox [Homo sapiens (human)] - Gene

Summary

Official Symbol: CRXprovided by HGNC
Official Full Name: cone-rod homeoboxprovided by HGNC
Primary source: HGNC:HGNC:2383
See related: Ensembl:ENSG00000105392 MIM:602225; AllianceGenome:HGNC:2383
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CRD; LCA7; OTX3; CORD2
Summary: The protein encoded by this gene is a photoreceptor-specific transcription factor which plays a role in the differentiation of photoreceptor cells. This homeodomain protein is necessary for the maintenance of normal cone and rod function. Mutations in this gene are associated with photoreceptor degeneration, Leber congenital amaurosis type III and the autosomal dominant cone-rod dystrophy 2. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.33

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (47821937..47843324)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (50652778..50674184)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (48325194..48346581)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model.
Title: Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model.
Downregulation of CRX, a Group 3-specific oncogenic transcription factor, inhibits TGF-beta/activin signaling in medulloblastoma cells.
Title: Downregulation of CRX, a Group 3-specific oncogenic transcription factor, inhibits TGF-β/activin signaling in medulloblastoma cells.
Distantly Metastatic Retinoblastoma to Soft Tissue and Bone: A Challenging Diagnosis Highlighting the Utility of CRX.
Title: Distantly Metastatic Retinoblastoma to Soft Tissue and Bone: A Challenging Diagnosis Highlighting the Utility of CRX.
Clinical and Genetic Characteristics of 18 Patients from 13 Japanese Families with CRX-associated retinal disorder: Identification of Genotype-phenotype Association.
Title: Clinical and Genetic Characteristics of 18 Patients from 13 Japanese Families with CRX-associated retinal disorder: Identification of Genotype-phenotype Association.
Heterozygous CRX deletion is associated with recurrent arcuate retinopathy in familial cone-rod dystrophy.
Title: A recurrent arcuate retinopathy in familial cone-rod dystrophy secondary to heterozygous CRX deletion.
Incomplete penetrance of CRX gene for autosomal dominant form is associated cone-rod dystrophy.
Title: Incomplete penetrance of CRX gene for autosomal dominant form of cone-rod dystrophy.
two known retinal dystrophy genes, PRPH2 and CRX, achieved study-wide significance (p < 1.33 x 10-6) under a dominant disease model
Title: A case-control collapsing analysis identifies retinal dystrophy genes associated with ophthalmic disease in patients with no pathogenic ABCA4 variants.
most heterozygous pathogenic variants in CRX are associated with autosomal dominant retinal degeneration, a homozygous c.268C>T (p.Arg90Trp) substitution and homozygous complete deletion of CRX have been reported to cause Leber congenital amaurosis. In conclusion, many rare missense variants and some truncating variants in CRX are likely benign.
Title: Pathogenicity discrimination and genetic test reference for CRX variants based on genotype-phenotype analysis.
Study in Lebanese family with 3 affected individuals report for a first time a novel, complete homozygous 56,000 bp deletion of CRX in Leber congenital amaurosis.
Title: A complete, homozygous CRX deletion causing nullizygosity is a new genetic mechanism for Leber congenital amaurosis.
The five patients with bull's-eye maculopathy along with a negative ERG had differing genotypes. Mutations were found in the CRX gene (2 patients), the ABCA4 gene (1 patient), and the GUCY2D gene (2 patients).
Title: Retinal dystrophies with bull's-eye maculopathy along with negative ERGs.

Submit: New GeneRIF Correction See all GeneRIFs (46)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cone-rod dystrophy 2 MedGen: C3489532 OMIM: 120970 GeneReviews: Not available	Compare labs
Leber congenital amaurosis 7 MedGen: C3151192 OMIM: 613829 GeneReviews: Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview	Compare labs
Retinitis pigmentosa MedGen: C0035334 OMIM: 268000 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S902 (e-PCR), detects polymorphism
- UniSTS:30729

G27385 (e-PCR)
- UniSTS:8722

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

Crx (e-PCR), detects polymorphism
- UniSTS:536452

D11S3114 (e-PCR)
- UniSTS:152207

G42186 (e-PCR)
- UniSTS:105104

Crx (e-PCR), detects polymorphism
- UniSTS:546710

RH78183 (e-PCR)
- UniSTS:24745

GDB:631813 (e-PCR)
- UniSTS:158430

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables leucine zipper domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info
part_of chromatin	ISA Inferred from Sequence Alignment more info
part_of chromatin	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: cone-rod homeobox protein

Names: orthodenticle homeobox 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.