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

Summary

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: mouse all
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Genomic context

Location:: 15q23

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (71810554..71818253)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (69629504..69637203)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (72102894..72110594)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Loss of an Orphan Nuclear Receptor NR2E3 Augments Wnt/beta-catenin Signaling via Epigenetic Dysregulation that Enhances Sp1-beta catenin-p300 Interactions in Hepatocellular Carcinoma.
Title: The Loss of an Orphan Nuclear Receptor NR2E3 Augments Wnt/β-catenin Signaling via Epigenetic Dysregulation that Enhances Sp1-β catenin-p300 Interactions in Hepatocellular Carcinoma.
NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development.
Title: NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development.
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.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (53)

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 EBI GWAS CatalogPubMed

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

NR2E3_2317 (e-PCR)
- UniSTS:280877

PMC21774P1 (e-PCR)
- UniSTS:272068

PMC21774P2 (e-PCR)
- UniSTS:272069

PMC21774P3 (e-PCR)
- UniSTS:272070

MARC_16201-16202:1030023389:1 (e-PCR)
- UniSTS:267990

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 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	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	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 receptor 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

NG_009113.2 RefSeqGene

Range

5000..12699

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

71810554..71818253

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

69629504..69637203

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.