NR0B2

nuclear receptor subfamily 0 group B member 2, the group of Nuclear receptor subfamily 0 group B

Basic information

Region (hg38): 1:26911488-26913975

Links

ENSG00000131910 ∙ NCBI:8431 ∙ OMIM:604630 ∙ HGNC:7961 ∙ Uniprot:Q15466 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NR0B2 gene.

• Obesity (1 variants)
• APC-mutation negative familial colorectal cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR0B2 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				11		11
missense			47		3	50
nonsense			2			2
start loss						0
frameshift	1	2	1			4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	2	50	11	3

Highest pathogenic variant AF is 0.0000394

Variants in NR0B2

This is a list of pathogenic ClinVar variants found in the NR0B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26911850-T-C		NR0B2-related disorder	Uncertain significance (Aug 31, 2022)
1-26911864-TC-T			Uncertain significance (Apr 06, 2022)
1-26911868-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-26911870-A-G		Inherited obesity • NR0B2-related disorder	Uncertain significance (Dec 20, 2023)
1-26911880-C-T		NR0B2-related disorder	Uncertain significance (Nov 11, 2022)
1-26911885-T-C		NR0B2-related disorder • not specified	Uncertain significance (Jan 17, 2024)
1-26911901-T-C		NR0B2-related disorder	Uncertain significance (Jul 21, 2023)
1-26911907-G-A		Obesity • NR0B2-related disorder • not specified	Uncertain significance (Jan 30, 2024)
1-26911947-G-A			Likely benign (May 23, 2023)
1-26911960-G-A			Benign (Apr 22, 2023)
1-26911972-C-T		NR0B2-related disorder	Uncertain significance (Dec 18, 2023)
1-26911981-C-T		NR0B2-related disorder	Uncertain significance (Oct 20, 2023)
1-26911982-G-A		Inherited obesity	Uncertain significance (May 17, 2022)
1-26911987-T-C		NR0B2-related disorder	Uncertain significance (Feb 23, 2024)
1-26911994-C-T		NR0B2-related disorder	Uncertain significance (Dec 11, 2022)
1-26912001-C-T		NR0B2-related disorder	Uncertain significance (Oct 21, 2023)
1-26912036-C-A		Obesity, mild, early-onset • not specified	Uncertain significance (May 04, 2022)
1-26912057-T-A		not specified	Uncertain significance (Jun 10, 2024)
1-26912066-C-T			Uncertain significance (Aug 16, 2023)
1-26913409-C-T		not specified • NR0B2-related disorder	Conflicting classifications of pathogenicity (Jan 19, 2024)
1-26913411-G-T		not specified	Uncertain significance (Aug 14, 2023)
1-26913413-G-T		Obesity	Uncertain significance (Jul 02, 2021)
1-26913420-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-26913429-C-G		not specified	Benign (Jan 31, 2024)
1-26913444-T-C		Inherited obesity	Uncertain significance (Apr 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR0B2	protein_coding	protein_coding	ENST00000254227	2	2478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000834	0.324	125558	0	190	125748	0.000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.250	146	155	0.944	0.00000928	1636
Missense in Polyphen		43	45.046	0.95459		574
Synonymous	1.03	54	64.5	0.838	0.00000354	573
Loss of Function	0.180	8	8.57	0.934	4.50e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00752	0.00726
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00752	0.00726
South Asian	0.00112	0.00111
Other	0.000731	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional regulator. Acts as a negative regulator of receptor-dependent signaling pathways. Specifically inhibits transactivation of the nuclear receptor with whom it interacts. Inhibits transcriptional activity of NEUROD1 on E-box- containing promoter by interfering with the coactivation function of the p300/CBP-mediated transcription complex for NEUROD1. {ECO:0000269|PubMed:14752053}.
• Disease: DISEASE: Obesity (OBESITY) [MIM:601665]: A condition characterized by an increase of body weight beyond the limitation of skeletal and physical requirements, as the result of excessive accumulation of body fat. {ECO:0000269|PubMed:11136233}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Bile secretion - Homo sapiens (human);NHR;Androgen receptor signaling pathway;Farnesoid X Receptor Pathway;Estrogen Receptor Pathway;Nuclear Receptors Meta-Pathway;Steatosis AOP;Gene expression (Transcription);mechanism of gene regulation by peroxisome proliferators via ppara;Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;AndrogenReceptor;Validated nuclear estrogen receptor alpha network;Validated nuclear estrogen receptor beta network (Consensus)

Recessive Scores

• pRec: 0.661

Intolerance Scores

• loftool: 0.359
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.676
• hipred: N
• hipred_score: 0.451
• ghis: 0.461

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: Nr0b2
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; normal phenotype; reproductive system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;Notch signaling pathway;cholesterol metabolic process;response to glucose;positive regulation of gene expression;negative regulation of gene expression;animal organ regeneration;positive regulation of insulin secretion;steroid hormone mediated signaling pathway;negative regulation of DNA-binding transcription factor activity
• Cellular component: nucleus;nucleoplasm;cytoplasm;protein-containing complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;steroid hormone receptor activity;transcription corepressor activity;protein binding;transcription factor binding;protein domain specific binding;protein homodimerization activity;peroxisome proliferator activated receptor binding;protein-containing complex binding;retinoid X receptor binding;thyroid hormone receptor binding