ARNT
Basic information
Region (hg38): 1:150809713-150876708
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 17 | 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 |
---|---|---|---|---|
1-150812070-T-C | not specified | Uncertain significance (Oct 19, 2024) | ||
1-150812086-G-C | not specified | Uncertain significance (Nov 13, 2024) | ||
1-150813249-G-C | not specified | Uncertain significance (Aug 22, 2023) | ||
1-150814091-C-T | not specified | Uncertain significance (Nov 20, 2024) | ||
1-150814097-G-A | not specified | Uncertain significance (Jul 19, 2022) | ||
1-150814127-G-A | not specified | Uncertain significance (Aug 01, 2024) | ||
1-150814154-A-G | not specified | Uncertain significance (Aug 28, 2024) | ||
1-150814193-C-G | not specified | Uncertain significance (Nov 26, 2024) | ||
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) | ||
1-150817094-T-C | not specified | Uncertain significance (Oct 24, 2024) | ||
1-150817097-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
1-150817408-C-T | Benign/Likely benign (Apr 01, 2023) | |||
1-150817426-G-C | not specified | Uncertain significance (Jul 27, 2024) | ||
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) | ||
1-150823210-T-C | not specified | Uncertain significance (Nov 28, 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) |
GnomAD
Source:
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:
- 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