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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10002
Gene name	Nuclear receptor subfamily 2 group E member 3
Gene symbol	NR2E3
Synonyms (NCBI Gene)	ESCSPNRRNRRP37rd7
Chromosome	15
Chromosome location	15q23
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

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

Show/Hide all (22)

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

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

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

695

Show/Hide Causal Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive retinitis pigmentosa	Likely pathogenic; Pathogenic	rs28937873	RCV001257807
Color vision defect	Likely pathogenic; Pathogenic	rs2723341	RCV000626919
Cone-rod dystrophy	Likely pathogenic; Pathogenic	rs2723341, rs750740765	RCV000678584 RCV000678585
Enhanced S-cone syndrome	Likely pathogenic; Pathogenic	rs757665544, rs760771835, rs1567160201, rs774102273, rs2140288872, rs1298419011, rs1449781976, rs2140290184, rs375133059, rs1448244599, rs202098481, rs2723341, rs527236086, rs730882149, rs35004053 View all (54 more)	RCV001836305 RCV003469626 RCV001831356 RCV001831369 RCV003462964 RCV004570956 RCV003471128 RCV003471100 RCV003471136 RCV003471138 RCV003471172 RCV003470967 RCV000670387 RCV005003509 RCV003465928 RCV003465929 RCV004572744 RCV000005864 RCV003468851 RCV003468852 RCV003989478 RCV003465800 RCV003464580 RCV000005866 RCV000005867 RCV000005868 RCV000005869 RCV005632167 RCV003465847 RCV003337957 RCV003471599 RCV003471600 RCV003471601 RCV003463205 RCV003471602 RCV003471603 RCV003471604 RCV003476581 RCV003463207 RCV003471605 RCV003471606 RCV003471607 RCV003463208 RCV003471608 RCV003463209 RCV003471609 RCV003471610 RCV003471611 RCV005003673 RCV004574395 RCV004574396 RCV004574397 RCV004574399 RCV004574400 RCV004574401 RCV004574402 RCV004574403 RCV003464083 RCV003464084 RCV000667010 RCV001830476 RCV003467321 RCV003461304 RCV001003095 RCV005633802 RCV001832466 RCV003462615 RCV001833644 RCV001827335 RCV001836119 RCV001833696 RCV003469276 RCV003469283 RCV004570606
Goldmann-Favre syndrome	Pathogenic; Likely pathogenic	rs730882149, rs2723341, rs104894493, rs28937873, rs377257254, rs759339012	RCV001449814 RCV001275369 RCV001449793 RCV000005870 RCV001449815 RCV001275375
Horizontal nystagmus	Likely pathogenic; Pathogenic	rs2723341	RCV000626919
Leber congenital amaurosis	Pathogenic	rs574936510	RCV000678583
NR2E3-related disorder	Pathogenic; Likely pathogenic	rs774102273, rs527236086, rs35004053, rs2723341, rs104894492, rs104894493, rs28937873, rs2543253260, rs759339012	RCV004531189 RCV004532584 RCV004536548 RCV000261643 RCV004732530 RCV000261496 RCV000393548 RCV004531612 RCV004535917
Ocular albinism	Likely pathogenic; Pathogenic	rs2723341	RCV002243841
Retinal disorder	Likely pathogenic; Pathogenic	rs121912631	RCV006261933
Retinal dystrophy	Likely pathogenic; Pathogenic	rs121912631, rs750931603, rs527236086, rs35004053, rs2723341, rs786205493, rs368098126, rs2054207798, rs104894492, rs104894493, rs28937873, rs766096417, rs377257254, rs1555454566, rs750740765 View all (8 more)	RCV003888089 RCV003888946 RCV001075734 RCV004817197 RCV000505031 RCV004815268 RCV001074909 RCV004817083 RCV003887854 RCV001075864 RCV001074891 RCV001075751 RCV000504861 RCV000504973 RCV001074892 RCV004817918 RCV004817917 RCV001075832 RCV004818007 RCV001073492 RCV001075623 RCV001075821 RCV001075776 RCV001074489
Retinitis pigmentosa	Pathogenic; Likely pathogenic	rs774102273, rs527236086, rs2723341, rs368098126, rs104894492, rs28937873, rs121912631, rs1418275818, rs766096417, rs377257254, rs1555454566, rs759339012, rs1595956455, rs1595956595, rs776270511 View all (4 more)	RCV005057350 RCV000132672 RCV000787627 RCV000787632 RCV003323352 RCV000787633 RCV000787628 RCV003324704 RCV001003093 RCV001724033 RCV001003092 RCV000787629 RCV000787630 RCV000787631 RCV001003094 RCV001003096 RCV001199716 RCV001199488 RCV004768857
Retinitis pigmentosa 37	Likely pathogenic; Pathogenic	rs527236086, rs776270511, rs730882149, rs766232933, rs2723341, rs786205493, rs368098126, rs761628767, rs104894493, rs28937873, rs121912631, rs1567160967, rs2543254500, rs1246315416, rs766096417 View all (6 more)	RCV000670387 RCV002250881 RCV000162027 RCV005002945 RCV000185571 RCV001376479 RCV005008095 RCV001029779 RCV000668029 RCV000668086 RCV000005871 RCV000005872 RCV005003059 RCV005003643 RCV005003673 RCV002226466 RCV001376214 RCV000667010 RCV005004357 RCV006448603 RCV001593257 RCV005012547
Visual impairment	Likely pathogenic; Pathogenic	rs2723341	RCV000626919

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormality of the eye	Conflicting classifications of pathogenicity	rs772881093	RCV000504667
Atypical retinitis pigmentosa	Conflicting classifications of pathogenicity	rs770937516	RCV005419674
Optic atrophy	Uncertain significance; Conflicting classifications of pathogenicity	rs186714117, rs375133059	RCV004816505 RCV004818081
Retinitis Pigmentosa, Recessive	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs1805020, rs1805021, rs1805022, rs558123422, rs767828150, rs779518180, rs376114936, rs769154628, rs184906734, rs779157022, rs185349250, rs886051456, rs886051458, rs138513681, rs886051449 View all (18 more)	RCV000311274 RCV000269886 RCV000283298 RCV000331700 RCV000369444 RCV000321954 RCV000334655 RCV000352384 RCV000312701 RCV000358459 RCV000316892 RCV000386401 RCV000288328 RCV000402175 RCV000342126 RCV000302548 RCV000352902 RCV000389820 RCV000343027 RCV000391846 RCV000368328 RCV000295214 RCV000317994 RCV000401371 RCV000303540 RCV000362162 RCV000267190 RCV000406933 RCV000354670 RCV000290651 RCV000383869 RCV000344581 RCV000364056 RCV000351707

Show/Hide Text Mining Associations (34)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)