NR2C2

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

Basic information

Region (hg38): 3:14947582-15053600

Previous symbols: [ "TR4" ]

Links

ENSG00000177463 ∙ NCBI:7182 ∙ OMIM:601426 ∙ HGNC:7972 ∙ Uniprot:P49116 ∙ 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 NR2C2 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR2C2 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in NR2C2

This is a list of pathogenic ClinVar variants found in the NR2C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-15003970-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-15003979-G-A		not specified	Uncertain significance (Apr 11, 2023)
3-15013691-G-A		not specified	Uncertain significance (Nov 22, 2023)
3-15016180-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-15023315-T-A			Benign (May 08, 2018)
3-15030298-C-T		not specified	Uncertain significance (Mar 22, 2023)
3-15030397-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-15052467-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-15053465-A-G		not specified	Uncertain significance (Jun 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR2C2	protein_coding	protein_coding	ENST00000323373	14	106017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00108	125736	0	4	125740	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.18	195	366	0.532	0.0000215	4040
Missense in Polyphen		17	100.98	0.16835		1073
Synonymous	-0.523	141	133	1.06	0.00000765	1203
Loss of Function	4.61	2	28.6	0.0698	0.00000130	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan nuclear receptor that can act as a repressor or activator of transcription. An important repressor of nuclear receptor signaling pathways such as retinoic acid receptor, retinoid X, vitamin D3 receptor, thyroid hormone receptor and estrogen receptor pathways. May regulate gene expression during the late phase of spermatogenesis. Together with NR2C1, forms the core of the DRED (direct repeat erythroid-definitive) complex that represses embryonic and fetal globin transcription including that of GATA1. Binds to hormone response elements (HREs) consisting of two 5'-AGGTCA-3' half site direct repeat consensus sequences. Plays a fundamental role in early embryonic development and embryonic stem cells. Required for normal spermatogenesis and cerebellum development. Appears to be important for neurodevelopmentally regulated behavior (By similarity). Activates transcriptional activity of LHCG. Antagonist of PPARA-mediated transactivation. {ECO:0000250, ECO:0000269|PubMed:10347174, ECO:0000269|PubMed:10644740, ECO:0000269|PubMed:17974920, ECO:0000269|PubMed:7779113, ECO:0000269|PubMed:9556573}.
• Pathway: NHR;Androgen receptor signaling pathway;Nuclear Receptors;Hypothesized Pathways in Pathogenesis of Cardiovascular Disease;EMT transition in Colorectal Cancer;Gene expression (Transcription);p38 mapk signaling pathway;Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;AndrogenReceptor;tgf beta signaling pathway;TNFalpha;Regulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.0630
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.825
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nr2c2
• Phenotype: endocrine/exocrine gland 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; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;transcription initiation from RNA polymerase II promoter;spermatogenesis;nervous system development;cell differentiation;steroid hormone mediated signaling pathway;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;steroid hormone receptor activity;transcription coactivator activity;protein binding;zinc ion binding;signaling receptor activity;sequence-specific DNA binding;protein heterodimerization activity