Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	10002
Gene name Gene Name - the full gene name approved by the HGNC.	Nuclear receptor subfamily 2 group E member 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NR2E3
Synonyms (NCBI Gene) Gene synonyms aliases	ESCS, PNR, RNR, RP37, rd7
Chromosome Chromosome number	15
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	15q23
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(28)

SNP ID	Visualize variation	Clinical significance	Consequence
rs2723341	A>C	Pathogenic, pathogenic-likely-pathogenic, likely-pathogenic	Splice acceptor variant
rs28937873	G>A	Likely-pathogenic, pathogenic, pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs104894492	C>A,T	Pathogenic	Missense variant, coding sequence variant, synonymous variant
rs104894493	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs112520386	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs121912631	G>A,T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs368098126	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs377257254	C>A,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs527236086	C>T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs574936510	TTT>-,T,TT	Pathogenic	Inframe deletion, genic downstream transcript variant, coding sequence variant, frameshift variant
rs730882149	GC>AGTGTGCCTCCAGTGCCTCGCTCCA	Pathogenic	Frameshift variant, coding sequence variant
rs750740765	TC>-	Pathogenic	Frameshift variant, coding sequence variant
rs752883545	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs759339012	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs761628767	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs766096417	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs767442358	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs772881093	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs776270511	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs786205493	C>A,G,T	Likely-pathogenic	Synonymous variant, stop gained, coding sequence variant, missense variant
rs1555454566	ACGGCTGCA>-	Likely-pathogenic, pathogenic	Inframe deletion, coding sequence variant
rs1567159701	GCAGCGGCT>-	Pathogenic	Coding sequence variant, inframe deletion
rs1567160967	TGCAG>-	Pathogenic	Coding sequence variant, stop gained
rs1595956148	C>T	Pathogenic	Coding sequence variant, stop gained
rs1595956455	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1595956595	->A	Likely-pathogenic	Coding sequence variant, stop gained
rs1595956702	G>C	Pathogenic	Splice donor variant
rs1595957521	G>C	Pathogenic	Coding sequence variant, missense variant

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miRTarBase ID	miRNA	Experiments
MIRT1192479	hsa-miR-320a	CLIP-seq
MIRT1192480	hsa-miR-320b	CLIP-seq
MIRT1192481	hsa-miR-320c	CLIP-seq
MIRT1192482	hsa-miR-320d	CLIP-seq
MIRT1192483	hsa-miR-4260	CLIP-seq
MIRT1192484	hsa-miR-4283	CLIP-seq
MIRT1192485	hsa-miR-4429	CLIP-seq
MIRT1192486	hsa-miR-4489	CLIP-seq
MIRT1192483	hsa-miR-4260	CLIP-seq
MIRT1192484	hsa-miR-4283	CLIP-seq
MIRT1192486	hsa-miR-4489	CLIP-seq
MIRT2284638	hsa-miR-4795-3p	CLIP-seq
MIRT2284639	hsa-miR-582-5p	CLIP-seq
MIRT2391717	hsa-miR-1293	CLIP-seq
MIRT2391718	hsa-miR-3178	CLIP-seq
MIRT2391719	hsa-miR-4481	CLIP-seq
MIRT2391720	hsa-miR-4483	CLIP-seq
MIRT2391721	hsa-miR-4745-5p	CLIP-seq
MIRT2391722	hsa-miR-4758-5p	CLIP-seq
MIRT2391723	hsa-miR-541	CLIP-seq
MIRT2391724	hsa-miR-654-5p	CLIP-seq
MIRT2284638	hsa-miR-4795-3p	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
CRX	Activation	18294621
NRL	Activation	18294621

Show/Hide all(37)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	10220376
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IMP	22174013
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003707	Function	Nuclear steroid receptor activity	IEA
GO:0004879	Function	Nuclear receptor activity	IBA
GO:0004879	Function	Nuclear receptor activity	TAS	10220376
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	10220376
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005667	Component	Transcription regulator complex	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0007165	Process	Signal transduction	TAS	10220376
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	10220376
GO:0007602	Process	Phototransduction	TAS	10220376
GO:0008270	Function	Zinc ion binding	IEA
GO:0008283	Process	Cell population proliferation	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0030182	Process	Neuron differentiation	IBA
GO:0030518	Process	Nuclear receptor-mediated steroid hormone signaling pathway	IEA
GO:0030522	Process	Intracellular receptor signaling pathway	IEA
GO:0042462	Process	Eye photoreceptor cell development	IEA
GO:0043565	Function	Sequence-specific DNA binding	IDA	10220376
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	22174013
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	22174013
GO:0046872	Function	Metal ion binding	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA

MIM	HGNC	e!Ensembl
604485	7974	ENSG00000278570

Protein

UniProt ID

Q9Y5X4

Protein name

Photoreceptor-specific nuclear receptor (Nuclear receptor subfamily 2 group E member 3) (Retina-specific nuclear receptor)

Protein 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,

PDB

4LOG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00105	zf-C4	45 → 115	Zinc finger, C4 type (two domains)	Domain
PF00104	Hormone_recep	205 → 395	Ligand-binding domain of nuclear hormone receptor	Domain

Tissue specificity

TISSUE SPECIFICITY: Eye specific; found solely in the outer nuclear layer of the adult neurosensory retina, where the nuclei of cone and rod photoreceptors reside. {ECO:0000269|PubMed:15689355}.

Sequence

METRPTALMSSTVAAAAPAAGAASRKESPGRWGLGEDPTGVSPSLQCRVCGDSSSGKHYG
IYACNGCSGFFKRSVRRRLIYRCQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQN
ERQPRSTAQVHLDSMESNTESRPESLVAPPAPAGRSPRGPTPMSAARALGHHFMASLITA
ETCAKLEPEDADENIDVTSNDPEFPSSPYSSSSPCGLDSIHETSARLLFMAVKWAKNLPV
FSSLPFRDQVILLEEAWSELFLLGAIQWSLPLDSCPLLAPPEASAAGGAQGRLTLASMET
RVLQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQSQVMLSQHSKAH
HPSQPVRFGKLLLLLPSLRFITAERIELLFFRKTIGNTPMEKLLCDMFKN

Sequence length

410

Interactions

View interactions

	Reactome
			Nuclear Receptor transcription pathway

Show/Hide Causal Diseases (6)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Enhanced S-Cone Syndrome	enhanced s-cone syndrome	rs761628767, rs759339012, rs2723341, rs104894492, rs990307718, rs1555454566, rs2054187597, rs2054201689, rs2054202316, rs2054184757, rs104894493, rs1279558746, rs750740765, rs786205493, rs766096417 View all (9 more)	N/A
Goldmann-Favre Syndrome	goldmann-favre syndrome	rs730882149, rs104894493, rs377257254, rs759339012, rs28937873	N/A
retinal dystrophy	Retinal dystrophy	rs759339012, rs28937873, rs2054237722, rs2054201689, rs104894492, rs766096417, rs1555454566, rs2723341, rs1595956595, rs121912631, rs104894493, rs1489149705, rs750740765, rs377257254, rs786205493 View all (5 more)	N/A
Retinitis Pigmentosa	retinitis pigmentosa, Retinitis pigmentosa 37	rs2054205040, rs1555454566, rs761628767, rs28937873, rs1595956455, rs2723341, rs121912631, rs1595956595, rs104894492, rs766096417, rs776270511, rs1567160967, rs786205493, rs527236086, rs1595957521 View all (8 more)	N/A
cone-rod dystrophy	Cone-rod dystrophy	rs750740765, rs2723341	N/A
Leber Congenital Amaurosis	leber congenital amaurosis	rs574936510	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Breast Neoplasms	Associate	22174013, 24066170
Carcinoma Hepatocellular	Associate	28878246
Cataract	Associate	26910043
Color Vision Defects	Associate	15453866, 32881472
Cone Rod Dystrophies	Associate	21364904
Dentin Sensitivity	Associate	25703721
Disease	Associate	36260161
Enhanced S Cone Syndrome	Associate	11773633, 15453866, 17564971, 18835469, 19823680, 19852574, 21364904, 23604511, 23989059, 24069298, 24891813, 25703721, 27033713, 30285900, 30959774 View all (7 more)
Facial Dermatoses	Associate	24069298
Fibrosis	Associate	23989059
Genetic Diseases Inborn	Associate	11773633, 38453143
Hearing Loss Functional	Associate	33138239
Hepatolenticular Degeneration	Associate	36071243
Hypertensive Retinopathy	Associate	28300834, 31117170
Leber Congenital Amaurosis	Associate	24891813
Legius syndrome	Associate	36071243
Lipodystrophy Familial Partial	Associate	28300834
Macular Degeneration	Associate	23989059
Macular Edema	Associate	23989059, 37246744
Neoplasms	Associate	22025681, 24066170
Nerve Degeneration	Associate	11773633
Neurodegenerative Diseases	Associate	21364904
Night Blindness	Associate	26910043, 33138239
Night blindness congenital stationary	Associate	32881472
Photophobia	Associate	33138239
photopsia	Associate	33138239
Pigmentation Disorders	Associate	23989059
Retinal Degeneration	Associate	10220376, 11773633, 21364904, 24069298, 25703721, 31117170
Retinal Diseases	Associate	22025681, 24066170, 24069298, 28300834, 31083481, 38453143
Retinal Dystrophies	Associate	24891813, 27874104, 30285900, 32881472, 33007388, 36260161
Retinitis	Associate	11773633, 23989059, 30285900
Retinitis Pigmentosa	Associate	17564971, 19823680, 22128245, 22605927, 22661467, 23559859, 23950152, 24069298, 26910043, 28076437, 29034877, 31083481, 33007388
Retinoblastoma	Associate	10220376
Vision Disorders	Associate	18835469, 26910043, 33138239

NR2E3 (nuclear receptor subfamily 2 group E member 3)