NR2E1

nuclear receptor subfamily 2 group E member 1, the group of Nuclear receptor subfamily 2 group E

Basic information

Region (hg38): 6:108166022-108188805

Previous symbols: [ "TLX" ]

Links

ENSG00000112333 ∙ NCBI:7101 ∙ OMIM:603849 ∙ HGNC:7973 ∙ Uniprot:Q9Y466 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NR2E1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR2E1 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				3		3
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	12	4	0

Variants in NR2E1

This is a list of pathogenic ClinVar variants found in the NR2E1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-108166777-A-G		NR2E1-related disorder	Likely benign (Jun 06, 2019)
6-108168131-A-T		NR2E1-related disorder	Likely benign (Sep 17, 2019)
6-108171526-G-A		not specified	Uncertain significance (Oct 20, 2024)
6-108171543-A-G		NR2E1-related disorder	Likely benign (Jul 23, 2019)
6-108171601-C-G		not specified	Uncertain significance (Jun 16, 2023)
6-108174909-A-G		not specified	Uncertain significance (Feb 05, 2024)
6-108176522-G-A		NR2E1-related disorder	Likely benign (Sep 04, 2019)
6-108176579-G-A		NR2E1-related disorder	Likely benign (Mar 01, 2019)
6-108176607-T-C		not specified	Uncertain significance (Feb 22, 2023)
6-108176636-C-G		not specified	Uncertain significance (Sep 27, 2022)
6-108176649-C-G		not specified	Uncertain significance (May 27, 2022)
6-108178092-C-T		NR2E1-related disorder	Benign (Dec 02, 2019)
6-108180835-G-C		not specified	Uncertain significance (Jan 23, 2023)
6-108180852-T-C		not specified	Uncertain significance (Dec 16, 2022)
6-108180941-G-A		not specified	Uncertain significance (Jul 20, 2021)
6-108181582-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-108181593-G-A		not specified	Uncertain significance (Apr 19, 2023)
6-108181627-C-T		not specified	Uncertain significance (Mar 06, 2023)
6-108187308-A-G		not specified	Uncertain significance (Apr 04, 2023)
6-108187407-G-A		not specified	Uncertain significance (May 26, 2024)
6-108187411-A-G		not specified	Uncertain significance (Nov 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR2E1	protein_coding	protein_coding	ENST00000368986	9	22752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00136	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	111	219	0.506	0.0000122	2483
Missense in Polyphen		15	57.537	0.2607		712
Synonymous	1.08	76	88.9	0.855	0.00000509	768
Loss of Function	4.06	0	19.2	0.00	9.54e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half- site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). May be required to pattern anterior brain differentiation. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity (By similarity). May be involved in retinoic acid receptor (RAR) regulation in retinal cells. {ECO:0000250}.
• Pathway: NHR;Nuclear Receptors;Olfactory bulb development and olfactory learning;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.0514
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.658
• hipred: Y
• hipred_score: 0.837
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nr2e1
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;behavioral fear response;aggressive behavior;transcription initiation from RNA polymerase II promoter;nervous system development;visual perception;dentate gyrus development;amygdala development;olfactory bulb development;layer formation in cerebral cortex;forebrain generation of neurons;cerebral cortex neuron differentiation;anterior commissure morphogenesis;extracellular matrix organization;somatic stem cell population maintenance;social behavior;negative regulation of apoptotic process;steroid hormone mediated signaling pathway;cell fate commitment;negative regulation of neuron differentiation;positive regulation of angiogenesis;positive regulation of cell cycle;positive regulation of transcription by RNA polymerase II;negative regulation of astrocyte differentiation;regulation of dendrite morphogenesis;retina development in camera-type eye;regulation of timing of neuron differentiation;long-term synaptic potentiation;regulation of cell migration involved in sprouting angiogenesis;negative regulation of neural precursor cell proliferation;positive regulation of neural precursor cell proliferation;positive regulation of stem cell proliferation
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;steroid hormone receptor activity;protein binding;zinc ion binding;histone deacetylase binding;sequence-specific DNA binding