NR2C1

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

Basic information

Region (hg38): 12:95020229-95073628

Previous symbols: [ "TR2" ]

Links

ENSG00000120798 ∙ NCBI:7181 ∙ OMIM:601529 ∙ HGNC:7971 ∙ Uniprot:P13056 ∙ 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 NR2C1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR2C1 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		1
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	0

Variants in NR2C1

This is a list of pathogenic ClinVar variants found in the NR2C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-95022320-A-G		not specified	Uncertain significance (Dec 13, 2024)
12-95022326-C-T		not specified	Uncertain significance (Jan 23, 2025)
12-95022359-T-C		not specified	Uncertain significance (Dec 13, 2024)
12-95022395-C-T		not specified	Uncertain significance (Feb 13, 2025)
12-95025224-T-C		not specified	Uncertain significance (Jan 07, 2025)
12-95028390-G-A		not specified	Uncertain significance (Jan 17, 2025)
12-95031360-C-G		not specified	Uncertain significance (Apr 18, 2023)
12-95031361-T-C		not specified	Uncertain significance (May 29, 2024)
12-95031433-C-T		not specified	Uncertain significance (Dec 20, 2023)
12-95040485-T-A		not specified	Uncertain significance (Apr 20, 2023)
12-95040543-A-T		not specified	Uncertain significance (Dec 12, 2022)
12-95040570-A-G		not specified	Uncertain significance (Oct 20, 2024)
12-95049139-T-C		not specified	Likely benign (Oct 09, 2024)
12-95049147-T-C		not specified	Uncertain significance (Jul 20, 2022)
12-95049157-C-T		not specified	Uncertain significance (Oct 07, 2024)
12-95049167-C-T			Likely benign (Apr 01, 2022)
12-95049214-T-C		not specified	Uncertain significance (Feb 10, 2022)
12-95049226-C-T		not specified	Uncertain significance (Aug 23, 2021)
12-95051775-C-G		not specified	Uncertain significance (May 30, 2023)
12-95051785-C-T		not specified	Uncertain significance (Dec 02, 2024)
12-95051828-C-T		not specified	Uncertain significance (Feb 13, 2024)
12-95051929-C-A		not specified	Uncertain significance (Jan 23, 2024)
12-95057617-A-G		not specified	Uncertain significance (Sep 16, 2021)
12-95057627-C-G		not specified	Uncertain significance (Oct 27, 2022)
12-95057632-A-G		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR2C1	protein_coding	protein_coding	ENST00000333003	13	53475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.683	0.317	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	256	314	0.816	0.0000152	3965
Missense in Polyphen		91	145.01	0.62753		1825
Synonymous	1.62	88	110	0.803	0.00000568	1113
Loss of Function	4.34	7	34.5	0.203	0.00000198	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000249	0.000244
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000706	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000146	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan nuclear receptor. Binds the IR7 element in the promoter of its own gene in an autoregulatory negative feedback mechanism. Primarily repressor of a broad range of genes. Binds to hormone response elements (HREs) consisting of two 5'-AGGTCA-3' half site direct repeat consensus sequences. Together with NR2C2, forms the core of the DRED (direct repeat erythroid-definitive) complex that represses embryonic and fetal globin transcription. Also activator of OCT4 gene expression. May be involved in stem cell proliferation and differentiation. Mediator of retinoic acid- regulated preadipocyte proliferation. {ECO:0000269|PubMed:12093804, ECO:0000269|PubMed:17010934}.
• Pathway: NHR;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;AndrogenReceptor;Regulation of Androgen receptor activity;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.0729
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.192
• hipred: Y
• hipred_score: 0.825
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nr2c1
• Phenotype: hematopoietic system phenotype; normal phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;steroid hormone mediated signaling pathway;positive regulation of retinoic acid receptor signaling pathway
• Cellular component: nucleoplasm;PML body
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;steroid hormone receptor activity;protein binding;zinc ion binding;signaling receptor activity;protein homodimerization activity;histone deacetylase binding