NR1I2

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

Basic information

Region (hg38): 3:119780484-119818487

Links

ENSG00000144852 ∙ NCBI:8856 ∙ OMIM:603065 ∙ HGNC:7968 ∙ Uniprot:O75469 ∙ 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 NR1I2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR1I2 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				2	5	7
missense			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	27	4	5

Variants in NR1I2

This is a list of pathogenic ClinVar variants found in the NR1I2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119807296-C-T		not specified	Likely benign (May 31, 2022)
3-119807328-G-T		not specified	Uncertain significance (Jan 04, 2024)
3-119807341-G-A		not specified	Uncertain significance (Dec 16, 2023)
3-119807359-G-A		not specified	Uncertain significance (May 30, 2024)
3-119807374-C-T		not specified	Uncertain significance (Nov 22, 2023)
3-119807428-G-A		not specified	Uncertain significance (Jan 26, 2023)
3-119810111-C-A		not specified	Uncertain significance (Nov 30, 2022)
3-119810161-C-T		not specified	Uncertain significance (Feb 02, 2022)
3-119810178-C-T			Benign (Jun 29, 2018)
3-119811553-G-A		not specified	Uncertain significance (Sep 13, 2023)
3-119811559-G-A		not specified	Uncertain significance (Apr 20, 2023)
3-119811576-C-T			Benign (Mar 29, 2018)
3-119811586-C-T		not specified	Uncertain significance (Oct 03, 2023)
3-119811601-C-T		not specified	Uncertain significance (Apr 20, 2024)
3-119811608-G-C		not specified	Uncertain significance (Dec 15, 2022)
3-119811644-A-G		not specified	Uncertain significance (Jun 24, 2022)
3-119811691-T-G		not specified	Uncertain significance (Jan 22, 2024)
3-119811699-T-C			Benign (Aug 29, 2018)
3-119811700-A-G		not specified	Uncertain significance (May 01, 2024)
3-119812709-C-T			Likely benign (May 01, 2022)
3-119812713-G-A		not specified	Uncertain significance (Oct 26, 2021)
3-119812774-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-119812794-A-G		not specified	Uncertain significance (Jan 24, 2024)
3-119812813-G-A		not specified	Uncertain significance (Apr 19, 2024)
3-119812847-C-A			Likely benign (Jun 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR1I2	protein_coding	protein_coding	ENST00000337940	9	38002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.27e-9	0.459	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.622	307	278	1.10	0.0000175	3115
Missense in Polyphen		121	106.4	1.1372		1234
Synonymous	-1.06	121	107	1.13	0.00000663	911
Loss of Function	0.975	15	19.7	0.763	9.03e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000708	0.000704
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000544	0.000544
South Asian	0.000395	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nuclear receptor that binds and is activated by variety of endogenous and xenobiotic compounds. Transcription factor that activates the transcription of multiple genes involved in the metabolism and secretion of potentially harmful xenobiotics, drugs and endogenous compounds. Activated by the antibiotic rifampicin and various plant metabolites, such as hyperforin, guggulipid, colupulone, and isoflavones. Response to specific ligands is species-specific. Activated by naturally occurring steroids, such as pregnenolone and progesterone. Binds to a response element in the promoters of the CYP3A4 and ABCB1/MDR1 genes. {ECO:0000269|PubMed:11297522, ECO:0000269|PubMed:11668216, ECO:0000269|PubMed:12578355, ECO:0000269|PubMed:18768384, ECO:0000269|PubMed:19297428, ECO:0000269|PubMed:9727070}.
• Pathway: Carbamazepine Pathway, Pharmacokinetics;Taxane Pathway, Pharmacokinetics;Metformin Pathway, Pharmacodynamic;Etoposide Pathway, Pharmacokinetics/Pharmacodynamics;NHR;Nuclear Receptors;Drug Induction of Bile Acid Pathway;Pregnane X Receptor pathway;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.650

Intolerance Scores

• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.86

Haploinsufficiency Scores

• pHI: 0.452
• hipred: N
• hipred_score: 0.354
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nr1i2
• Phenotype: homeostasis/metabolism 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)

Gene ontology

• Biological process: transcription initiation from RNA polymerase II promoter;xenobiotic metabolic process;signal transduction;multicellular organism development;steroid metabolic process;cell differentiation;intracellular receptor signaling pathway;exogenous drug catabolic process;xenobiotic transport;steroid hormone mediated signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;drug export
• Cellular component: nucleus;nucleoplasm;nuclear body;intermediate filament cytoskeleton;RNA polymerase II transcription factor complex
• Molecular function: transcription regulatory region sequence-specific DNA binding;RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;steroid hormone receptor activity;transcription coactivator activity;nuclear receptor activity;protein binding;transcription factor binding;drug binding;zinc ion binding;nuclear receptor transcription coactivator activity;signaling receptor activity