ARNT

aryl hydrocarbon receptor nuclear translocator, the group of PAS domain containing|Basic helix-loop-helix proteins

Basic information

Region (hg38): 1:150809713-150876708

Links

ENSG00000143437 ∙ NCBI:405 ∙ OMIM:126110 ∙ HGNC:700 ∙ Uniprot:P27540 ∙ 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 ARNT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARNT 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in ARNT

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

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

Position	Type	Phenotype	Significance	ClinVar
1-150813249-G-C		not specified	Uncertain significance (Aug 22, 2023)
1-150814091-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-150814097-G-A		not specified	Uncertain significance (Jul 19, 2022)
1-150814127-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-150816272-C-G		not specified	Uncertain significance (May 06, 2022)
1-150816344-A-G		not specified	Uncertain significance (Jun 02, 2024)
1-150816395-A-G		not specified	Uncertain significance (Jan 26, 2023)
1-150816806-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-150816812-G-T		not specified	Uncertain significance (Jul 26, 2022)
1-150817097-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-150817408-C-T			Benign/Likely benign (Apr 01, 2023)
1-150817966-T-C		not specified	Uncertain significance (Mar 29, 2024)
1-150817983-C-T		not specified	Uncertain significance (May 26, 2023)
1-150818010-C-T		not specified	Uncertain significance (Jun 19, 2024)
1-150829110-C-G		not specified	Uncertain significance (Aug 04, 2021)
1-150829113-T-C		not specified	Uncertain significance (Jul 20, 2022)
1-150829190-A-G		not specified	Uncertain significance (Apr 01, 2024)
1-150829946-G-T			Likely benign (Aug 15, 2018)
1-150829962-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-150829974-G-C		not specified	Uncertain significance (Jun 17, 2024)
1-150831893-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-150832391-C-T		not specified	Likely benign (Oct 10, 2023)
1-150834556-G-A		not specified	Uncertain significance (Feb 02, 2024)
1-150834637-C-T		not specified	Uncertain significance (Mar 29, 2024)
1-150842466-G-A		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARNT	protein_coding	protein_coding	ENST00000358595	22	67064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00419	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	309	442	0.700	0.0000234	5157
Missense in Polyphen		82	164.87	0.49738		1839
Synonymous	0.516	147	155	0.947	0.00000756	1550
Loss of Function	5.41	7	47.0	0.149	0.00000241	500

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000599	0.0000599
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000554	0.0000527
Middle Eastern	0.0000546	0.0000544
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for activity of the Ah (dioxin) receptor. This protein is required for the ligand-binding subunit to translocate from the cytosol to the nucleus after ligand binding. The complex then initiates transcription of genes involved in the activation of PAH procarcinogens. The heterodimer binds to core DNA sequence 5'-TACGTG-3' within the hypoxia response element (HRE) of target gene promoters and functions as a transcriptional regulator of the adaptive response to hypoxia (By similarity). The heterodimer ARNT:AHR binds to core DNA sequence 5'-TGCGTG-3' within the dioxin response element (DRE) of target gene promoters and activates their transcription (PubMed:28396409). {ECO:0000250|UniProtKB:P53762, ECO:0000269|PubMed:28396409}.
• Pathway: Renal cell carcinoma - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Diuretics Pathway, Pharmacodynamics;Angiogenesis;Aryl Hydrocarbon Receptor;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;Photodynamic therapy-induced HIF-1 survival signaling;Pathways in clear cell renal cell carcinoma;Type 2 papillary renal cell carcinoma;Regulation of gene expression by Hypoxia-inducible Factor;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Cellular response to hypoxia;ahr signal transduction pathway;hypoxia-inducible factor in the cardivascular system;Aryl hydrocarbon receptor signalling;Phase I - Functionalization of compounds;erythropoietin mediated neuroprotection through nf-kb;vegf hypoxia and angiogenesis;Cellular responses to stress;Endogenous sterols;Xenobiotics;Cytochrome P450 - arranged by substrate type;HIF-2-alpha transcription factor network;Biological oxidations;Metabolism;Hypoxic and oxygen homeostasis regulation of HIF-1-alpha;AndrogenReceptor;Cellular responses to external stimuli;Notch-mediated HES/HEY network;HIF-1-alpha transcription factor network (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.540
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.287
• hipred: Y
• hipred_score: 0.621
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arnt
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic 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); normal 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); reproductive system phenotype; 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); immune system phenotype; liver/biliary system phenotype; embryo phenotype

Gene ontology

• Biological process: response to hypoxia;embryonic placenta development;positive regulation of endothelial cell proliferation;transcription, DNA-templated;xenobiotic metabolic process;positive regulation of vascular endothelial growth factor production;cell differentiation;positive regulation of vascular endothelial growth factor receptor signaling pathway;positive regulation of protein sumoylation;mRNA transcription by RNA polymerase II;regulation of transcription from RNA polymerase II promoter in response to oxidative stress;positive regulation of erythrocyte differentiation;positive regulation of glycolytic process;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of hormone biosynthetic process;regulation of transcription from RNA polymerase II promoter in response to hypoxia
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear body;RNA polymerase II transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coactivator activity;aryl hydrocarbon receptor activity;protein binding;transcription factor binding;aryl hydrocarbon receptor binding;enhancer binding;protein homodimerization activity;sequence-specific DNA binding;protein heterodimerization activity;sequence-specific double-stranded DNA binding