Gene Gene information from NCBI Gene database.
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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
22
miRTarBase ID miRNA Experiments Reference
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
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
CRX Activation 18294621
NRL Activation 18294621
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
604485 7974 ENSG00000278570
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Sequence length 410
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Nuclear Receptor transcription pathway
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autosomal recessive retinitis pigmentosa Likely pathogenic; Pathogenic rs28937873 RCV001257807
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Color vision defect Likely pathogenic; Pathogenic rs2723341 RCV000626919
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone-rod dystrophy Likely pathogenic; Pathogenic rs2723341, rs750740765 RCV000678584
RCV000678585
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (69 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormality of the eye Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atypical retinitis pigmentosa Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHIES Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
GOUT GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Achromatopsia Achromatopsia BEFREE 12187427
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration BEFREE 24812550
★☆☆☆☆
Found in Text Mining only
Amaurosis congenita of Leber, type 1 Leber congenital amaurosis BEFREE 12187427
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 22174013, 24747967, 26901824
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 22174013, 24066170 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 28878246 Associate
★☆☆☆☆
Found in Text Mining only
Cataract Cataract Pubtator 26910043 Associate
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
Cholangiocarcinoma Cholangiocarcinoma BEFREE 21451941
★☆☆☆☆
Found in Text Mining only
Color Blindness, Blue Color blindness HPO_DG
★☆☆☆☆
Found in Text Mining only