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NR2E3 nuclear receptor subfamily 2 group E member 3 [ Homo sapiens (human) ]

Gene ID: 10002, updated on 5-Mar-2024

Summary

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Official Symbol
NR2E3provided by HGNC
Official Full Name
nuclear receptor subfamily 2 group E member 3provided by HGNC
Primary source
HGNC:HGNC:7974
See related
Ensembl:ENSG00000278570 MIM:604485; AllianceGenome:HGNC:7974
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
PNR; RNR; rd7; ESCS; RP37
Summary
This protein is part of a large family of nuclear receptor transcription factors involved in signaling pathways. Nuclear receptors have been shown to regulate pathways involved in embryonic development, as well as in maintenance of proper cell function in adults. Members of this family are characterized by discrete domains that function in DNA and ligand binding. This gene encodes a retinal nuclear receptor that is a ligand-dependent transcription factor. Defects in this gene are a cause of enhanced S cone syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See NR2E3 in Genome Data Viewer
Location:
15q23
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (71810554..71818253)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (69629504..69637203)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (72102894..72110594)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene thrombospondin type 1 domain containing 4 Neighboring gene uncharacterized LOC107984716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6615 Neighboring gene Sharpr-MPRA regulatory region 7020 Neighboring gene Sharpr-MPRA regulatory region 14876 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:71947880-71949079 Neighboring gene THSD4 antisense RNA 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:72053567-72054766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9705 Neighboring gene Sharpr-MPRA regulatory region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9709 Neighboring gene RNA, 5S ribosomal pseudogene 399 Neighboring gene myosin IXA Neighboring gene uncharacterized LOC107984713

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients. Al-Khuzaei S, et al. Genes (Basel), 2020 Oct 29. PMID 33138239, Free PMC Article
  2. Antisense Oligonucleotide-Based Downregulation of the G56R Pathogenic Variant Causing NR2E3-Associated Autosomal Dominant Retinitis Pigmentosa. Naessens S, et al. Genes (Basel), 2019 May 10. PMID 31083481, Free PMC Article
  3. Novel clinical findings in autosomal recessive NR2E3-related retinal dystrophy. Murro V, et al. Graefes Arch Clin Exp Ophthalmol, 2019 Jan. PMID 30324420
  4. Cone Vision Changes in the Enhanced S-Cone Syndrome Caused by NR2E3 Gene Mutations. Garafalo AV, et al. Invest Ophthalmol Vis Sci, 2018 Jul 2. PMID 29971438
  5. A novel NR2E3 gene mutation in autosomal recessive retinitis pigmentosa with cystic maculopathy. Mahajan D, et al. Acta Ophthalmol, 2018 Jun. PMID 29193891

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical and Genetic Features of NR2E3-Associated Retinopathy: A Report of Eight Families with a Longitudinal Study and Literature Review.
    Title: Clinical and Genetic Features of NR2E3-Associated Retinopathy: A Report of Eight Families with a Longitudinal Study and Literature Review.
  2. Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3): Role in Retinal Development and Disease.
    Title: Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3): Role in Retinal Development and Disease.
  3. Nr2e3 functional domain ablation by CRISPR-Cas9D10A identifies a new isoform and generates retinitis pigmentosa and enhanced S-cone syndrome models.
    Title: Nr2e3 functional domain ablation by CRISPR-Cas9D10A identifies a new isoform and generates retinitis pigmentosa and enhanced S-cone syndrome models.
  4. Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients.
    Title: Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients.
  5. Authors overexpressed wild type (WT) or mutant NR2E3 in RPE-1 cells, followed by AON treatment. Transcript and protein levels of WT and mutant NR2E3 were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot respectively.
    Title: Antisense Oligonucleotide-Based Downregulation of the G56R Pathogenic Variant Causing NR2E3-Associated Autosomal Dominant Retinitis Pigmentosa.
  6. our work revealed the novel role of NR2E3 as a positive upstream transcriptional regulator of AHR. Loss of NR2E3 caused repression of AHR by epigenetic reprogramming, which altered the active H3K4me2 status by modulating LSD1 distribution and activity.
    Title: Loss of NR2E3 represses AHR by LSD1 reprogramming, is associated with poor prognosis in liver cancer.
  7. Murine proof-of-concept studies suggest that clinical trials of patients with NR2E3 mutations may be forthcoming. Patterns of S-cone hyperfunction across the field would serve as a means to categorize patients as entry criteria or cohort selection in clinical trials.
    Title: Cone Vision Changes in the Enhanced S-Cone Syndrome Caused by NR2E3 Gene Mutations.
  8. Macular involvement was detectable in all the patients, and the abnormal foveal avascular zone (FAZ) supports the role of NR2E3 in retinal development.
    Title: Novel clinical findings in autosomal recessive NR2E3-related retinal dystrophy.
  9. A diagnosis of autosomal recessive retinitis pigmentosa (ARRP) with cystic maculopathy, caused by compound heterozygous mutation in the gene NR2E3, was made.
    Title: A novel NR2E3 gene mutation in autosomal recessive retinitis pigmentosa with cystic maculopathy.
  10. The patient presented characteristic symptoms, morphology and electrophysiological characteristics for S-cone deficiency syndrome and presented heterozygous for two mutations, one of which (c.790G>A; p.G264R in NR2E3), to our knowledge, has not been previously reported.
    Title: A new mutation in enhanced S-cone syndrome.
Submit: New GeneRIF Correction See all GeneRIFs (51)

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
Enhanced S-cone syndrome
MedGen: C1849394 OMIM: 268100 GeneReviews: Not available
Compare labs
Retinitis pigmentosa 37
MedGen: C1970163 OMIM: 611131 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC49976

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear steroid receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in eye photoreceptor cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phototransduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retina development in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
photoreceptor-specific nuclear receptor
Names
retina-specific nuclear receptor

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.

Genomic

  1. NG_009113.2 RefSeqGene

    Range
    5000..12699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014249.4 → NP_055064.1  photoreceptor-specific nuclear receptor isoform b

    See identical proteins and their annotated locations for NP_055064.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (b) contains a longer C-terminus compared to isoform a.
    Source sequence(s)
    AF121129, AL711747, AW080977, BU732726
    Consensus CDS
    CCDS73750.1
    UniProtKB/Swiss-Prot
    B6ZGU0, Q9UHM4, Q9Y5X4
    UniProtKB/TrEMBL
    A0A0F6T557
    Related
    ENSP00000482504.1, ENST00000617575.5
    Conserved Domains (2) summary
    cd06950
    Location:192 → 397
    NR_LBD_Tlx_PNR_like; The ligand binding domain of Tailless-like proteins, orphan nuclear receptors
    cd06970
    Location:39 → 130
    NR_DBD_PNR; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers

  2. NM_016346.4 → NP_057430.1  photoreceptor-specific nuclear receptor isoform a

    See identical proteins and their annotated locations for NP_057430.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes isoform a.
    Source sequence(s)
    AC104938, AF148128, KF495720
    Consensus CDS
    CCDS73751.1
    UniProtKB/TrEMBL
    A0A0F6T557, F1D8Q9
    Related
    ENSP00000479962.1, ENST00000621098.1
    Conserved Domains (2) summary
    cd06950
    Location:192 → 367
    NR_LBD_Tlx_PNR_like; The ligand binding domain of Tailless-like proteins, orphan nuclear receptors
    cd06970
    Location:39 → 130
    NR_DBD_PNR; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    71810554..71818253
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    69629504..69637203
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001281446.1: Suppressed sequence

    Description
    NM_001281446.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5X4.1 GenPept UniProtKB/Swiss-Prot:Q9Y5X4

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Miscellaneous