NR1I3

nuclear receptor subfamily 1 group I member 3, the group of Nuclear receptor subfamily 1 group I

Basic information

Region (hg38): 1:161229665-161238244

Links

ENSG00000143257 ∙ ∙ OMIM:603881 ∙ HGNC:7969 ∙ Uniprot:Q14994 ∙ 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 NR1I3 gene.

• not provided (12 variants)
• Inborn genetic diseases (12 variants)
• not specified (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR1I3 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	3	2	6
missense			14	3	1	18
nonsense						0
start loss			2			2
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	2	3
Total	0	0	18	7	5

Variants in NR1I3

This is a list of pathogenic ClinVar variants found in the NR1I3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161229690-A-G			Likely benign (Jan 01, 2024)
1-161229713-G-A			Likely benign (Mar 01, 2022)
1-161229789-G-A		not specified	Benign (Sep 06, 2013)
1-161229790-C-A		TOMM40L-related disorder	Likely benign (Oct 30, 2019)
1-161229842-C-A			Uncertain significance (Mar 01, 2018)
1-161229865-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-161229866-G-A		not specified	Benign (Sep 25, 2015)
1-161229905-T-G			Uncertain significance (Dec 18, 2013)
1-161229914-C-T		not specified	Benign/Likely benign (Aug 01, 2022)
1-161230796-T-G		not specified	Benign (Sep 04, 2013)
1-161230859-T-A		not specified	Uncertain significance (May 23, 2023)
1-161230888-A-G		not specified	Uncertain significance (Feb 09, 2022)
1-161230892-C-T		not specified	Uncertain significance (May 23, 2023)
1-161231133-C-T		not specified	Uncertain significance (Nov 22, 2021)
1-161231137-G-A		not specified	Uncertain significance (Jul 19, 2023)
1-161231182-A-T		not specified	Uncertain significance (Jun 29, 2023)
1-161231200-A-G		Kleefstra syndrome 1	Uncertain significance (Jul 13, 2012)
1-161231365-C-T		not specified	Uncertain significance (Jan 19, 2024)
1-161231366-G-A			Uncertain significance (Jan 07, 2015)
1-161232814-C-T			Uncertain significance (Oct 02, 2014)
1-161232815-G-A		not specified • NR1I3-related disorder	Benign (Oct 18, 2019)
1-161232834-T-C		not specified	Uncertain significance (Dec 28, 2023)
1-161232871-C-T		not specified	Uncertain significance (May 11, 2022)
1-161232889-G-A		not specified	Uncertain significance (Mar 11, 2024)
1-161232915-G-C		not specified	Likely benign (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR1I3	protein_coding	protein_coding	ENST00000367980	8	8637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.53e-8	0.557	125601	0	147	125748	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.811	177	210	0.843	0.0000120	2325
Missense in Polyphen		55	69.138	0.79551		794
Synonymous	0.0325	79	79.4	0.995	0.00000400	719
Loss of Function	1.06	14	19.0	0.738	0.00000116	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00240	0.00240
Ashkenazi Jewish	0.00	0.00
East Asian	0.000661	0.000653
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000604	0.000598
Middle Eastern	0.000661	0.000653
South Asian	0.000267	0.000261
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds and transactivates the retinoic acid response elements that control expression of the retinoic acid receptor beta 2 and alcohol dehydrogenase 3 genes. Transactivates both the phenobarbital responsive element module of the human CYP2B6 gene and the CYP3A4 xenobiotic response element.
• Pathway: Carbamazepine Pathway, Pharmacokinetics;NHR;Nuclear Receptors;Drug Induction of Bile Acid Pathway;Constitutive Androstane Receptor Pathway;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Gene expression (Transcription);mechanism of acetaminophen activity and toxicity;Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Glucocorticoid receptor regulatory network (Consensus)

Recessive Scores

• pRec: 0.348

Intolerance Scores

• loftool: 0.0107
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.44

Haploinsufficiency Scores

• pHI: 0.335
• hipred: N
• hipred_score: 0.360
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nr1i3
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: transcription initiation from RNA polymerase II promoter;signal transduction;multicellular organism development;cell differentiation;androgen receptor signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;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;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;nuclear receptor activity;transcription factor binding;zinc ion binding;nuclear receptor transcription coactivator activity;signaling receptor activity