NR2E3

nuclear receptor subfamily 2 group E member 3, the group of Nuclear receptor subfamily 2 group E

Basic information

Region (hg38): 15:71792638-71818259

Links

ENSG00000278570

∙ NCBI:10002 ∙ OMIM:604485 ∙ HGNC:7974 ∙ Uniprot:Q9Y5X4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Supportive), mode of inheritance: AD
Goldmann-Favre syndrome (Supportive), mode of inheritance: AR
enhanced S-cone syndrome (Strong), mode of inheritance: AR
enhanced S-cone syndrome (Strong), mode of inheritance: AR
retinitis pigmentosa 37 (Strong), mode of inheritance: AD
enhanced S-cone syndrome (Definitive), mode of inheritance: AR
retinitis pigmentosa 37 (Definitive), mode of inheritance: AD
retinitis pigmentosa 37 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Enhanced S-cone syndrome; Retinitis pigmentosa 37	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	13553271; 11071390; 10655056; 15229190; 17564971; 18294254; 20212206; 21364904; 22605927; 22807301

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NR2E3 gene.

not provided (53 variants)
Enhanced S-cone syndrome (10 variants)
Retinitis pigmentosa (3 variants)
Goldmann-Favre syndrome (2 variants)
Retinal dystrophy (2 variants)
Retinitis pigmentosa 37 (1 variants)
Leber congenital amaurosis (1 variants)
Cone-rod dystrophy (1 variants)
NR2E3-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR2E3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1 clinvar	11 clinvar	175 clinvar	4 clinvar	191
missense	6 clinvar	13 clinvar	198 clinvar	8 clinvar	1 clinvar	226
nonsense	10 clinvar	12 clinvar				22
start loss			3 clinvar			3
frameshift	35 clinvar	22 clinvar	1 clinvar			58
inframe indel		3 clinvar	4 clinvar			7
splice donor/acceptor (+/-2bp)	3 clinvar	13 clinvar	3 clinvar	1 clinvar		20
splice region		1	7	26		34
non coding		1 clinvar	28 clinvar	87 clinvar	5 clinvar	121
Total	54	65	248	271	10

Highest pathogenic variant AF is 0.0000526

Variants in NR2E3

This is a list of pathogenic ClinVar variants found in the NR2E3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
15-71810534-C-T	Enhanced S-cone syndrome • Retinitis pigmentosa	Likely benign (Jan 13, 2018)	888357
15-71810605-G-A	Retinitis Pigmentosa, Recessive • Enhanced S-cone syndrome	Uncertain significance (Jun 14, 2016)	317001
15-71810605-G-T	Enhanced S-cone syndrome • Retinitis Pigmentosa, Recessive • Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	317002
15-71810697-C-T	Retinitis Pigmentosa, Recessive • Enhanced S-cone syndrome	Uncertain significance (Jun 14, 2016)	317003
15-71810734-C-T	Enhanced S-cone syndrome;Retinitis pigmentosa 37	Uncertain significance (Mar 24, 2017)	550918
15-71810745-T-A		Uncertain significance (Oct 03, 2021)	1392332
15-71810745-T-C		Uncertain significance (Aug 27, 2021)	2157324
15-71810745-T-G	Enhanced S-cone syndrome	Uncertain significance (Jun 28, 2022)	942544
15-71810748-A-G		Uncertain significance (Sep 27, 2023)	2995211
15-71810752-C-T		Uncertain significance (Jun 10, 2022)	2421715
15-71810754-G-A		Uncertain significance (Sep 23, 2020)	2085676
15-71810766-T-C		Uncertain significance (Nov 13, 2019)	959898
15-71810767-G-A	Retinitis pigmentosa • Enhanced S-cone syndrome	Conflicting classifications of pathogenicity (Dec 03, 2023)	885248
15-71810772-GC-G		Pathogenic (Feb 03, 2022)	959947
15-71810774-T-G		Uncertain significance (Oct 04, 2023)	2989726
15-71810778-CA-C		Pathogenic (Nov 17, 2020)	1432619
15-71810779-A-G		Likely benign (Apr 06, 2021)	1152477
15-71810780-G-T	Enhanced S-cone syndrome	Uncertain significance (Mar 03, 2022)	1036822
15-71810782-G-A		Likely benign (Mar 02, 2021)	1090447
15-71810788-A-G	Enhanced S-cone syndrome;Retinitis pigmentosa 37	Likely benign (Jan 11, 2024)	552215
15-71810790-C-T	Goldmann-Favre syndrome	Uncertain significance (Aug 13, 2020)	990921
15-71810793-C-T	Goldmann-Favre syndrome • Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 17, 2022)	846003
15-71810794-G-A	Enhanced S-cone syndrome • NR2E3-related disorder	Likely benign (Dec 09, 2023)	713956
15-71810793-C-CAG		Pathogenic (Jul 28, 2021)	1453596
15-71810795-C-T		Uncertain significance (Aug 19, 2022)	2148289

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M- and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression. {ECO:0000269|PubMed:15689355, ECO:0000269|PubMed:24069298}.;
Disease: DISEASE: Enhanced S cone syndrome (ESCS) [MIM:268100]: Autosomal recessive retinopathy in which patients have increased sensitivity to blue light; perception of blue light is mediated by what is normally the least populous cone photoreceptor subtype, the S (short wavelength, blue) cones. ESCS is also associated with visual loss, with night blindness occurring from early in life, varying degrees of L (long, red)- and M (middle, green)-cone vision, and retinal degeneration. {ECO:0000269|PubMed:10655056, ECO:0000269|PubMed:11071390, ECO:0000269|PubMed:12963616, ECO:0000269|PubMed:15459973, ECO:0000269|PubMed:16225923, ECO:0000269|PubMed:18294254, ECO:0000269|PubMed:19006237, ECO:0000269|PubMed:24069298}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 37 (RP37) [MIM:611131]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:17564971, ECO:0000269|PubMed:19006237}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: NHR;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

pRec: 0.523

Haploinsufficiency Scores

pHI: 0.646
hipred
hipred_score
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.986

Mouse Genome Informatics

Gene name: Nr2e3
Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype;

Zebrafish Information Network

Gene name: nr2e3
Affected structure: parapineal organ
Phenotype tag: abnormal
Phenotype quality: has extra parts of type

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;signal transduction;visual perception;phototransduction;negative regulation of cell population proliferation;intracellular receptor signaling pathway;eye photoreceptor cell development;steroid hormone mediated signaling pathway;positive regulation of rhodopsin gene expression;positive regulation of transcription by RNA polymerase II;retina development in camera-type eye
Cellular component: nucleus;nucleoplasm;transcription factor complex
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;steroid hormone receptor activity;nuclear receptor activity;zinc ion binding;sequence-specific DNA binding