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Aliases for ARNT2 Gene

Aliases for ARNT2 Gene

  • Aryl Hydrocarbon Receptor Nuclear Translocator 2 2 3 5
  • Class E Basic Helix-Loop-Helix Protein 1 3 4
  • ARNT Protein 2 3 4
  • BHLHe1 3 4
  • KIAA0307 4
  • WEDAS 3

External Ids for ARNT2 Gene

Previous GeneCards Identifiers for ARNT2 Gene

  • GC15M076819
  • GC15P073853
  • GC15P078272
  • GC15P078412
  • GC15P078484
  • GC15P080696
  • GC15P057454

Summaries for ARNT2 Gene

Entrez Gene Summary for ARNT2 Gene

  • This gene encodes a member of the basic-helix-loop-helix-Per-Arnt-Sim (bHLH-PAS) superfamily of transcription factors. The encoded protein acts as a partner for several sensor proteins of the bHLH-PAS family, forming heterodimers with the sensor proteins that bind regulatory DNA sequences in genes responsive to developmental and environmental stimuli. Under hypoxic conditions, the encoded protein complexes with hypoxia-inducible factor 1alpha in the nucleus and this complex binds to hypoxia-responsive elements in enhancers and promoters of oxygen-responsive genes. A highly similar protein in mouse forms functional complexes with both aryl hydrocarbon receptors and Single-minded proteins, suggesting additional roles for the encoded protein in the metabolism of xenobiotic compounds and the regulation of neurogenesis, respectively. [provided by RefSeq, Dec 2013]

GeneCards Summary for ARNT2 Gene

ARNT2 (Aryl Hydrocarbon Receptor Nuclear Translocator 2) is a Protein Coding gene. Diseases associated with ARNT2 include Webb-Dattani Syndrome and Asperger Syndrome. Among its related pathways are Metabolism and Cytochrome P450 - arranged by substrate type. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and signal transducer activity. An important paralog of this gene is ARNT.

UniProtKB/Swiss-Prot for ARNT2 Gene

  • Transcription factor that plays a role in the development of the hypothalamo-pituitary axis, postnatal brain growth, and visual and renal function (PubMed:24022475). Specifically recognizes the xenobiotic response element (XRE).

Gene Wiki entry for ARNT2 Gene

Additional gene information for ARNT2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ARNT2 Gene

Genomics for ARNT2 Gene

Regulatory Elements for ARNT2 Gene

Enhancers for ARNT2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15H080476 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.8 +77.3 77275 9.5 SOX13 KLF1 KLF17 FEZF1 ZIC2 ZNF644 POLR2A FOS NR2F6 NR2F1 CEMIP ARNT2 GC15P080469 GC15M080508
GH15H080405 0.9 FANTOM5 dbSUPER 17.5 +1.1 1147 0.2 ZBTB48 ZNF341 SCRT2 ZIC2 ARNT2 ENSG00000258010
GH15H080595 1 ENCODE dbSUPER 15.5 +192.3 192320 1.9 SOX13 GATAD2A SAP130 FOXA3 HMG20A NR3C1 RARA TEAD3 NFIC JUND ARNT2 MIR5572 GC15P080662
GH15H080493 1.4 FANTOM5 Ensembl ENCODE dbSUPER 10.7 +90.2 90233 3.1 HNF1A JUND TEAD1 TEAD3 CEMIP ARNT2 GC15M080508 GC15P080469
GH15H080614 1.2 ENCODE dbSUPER 11.9 +211.7 211701 2.6 HDGF ZNF133 ZBTB7B ZNF207 ZNF662 ZNF592 ZFP41 MYNN SALL1 SUZ12 ENSG00000259649 ARNT2 RNU6-380P CEMIP MIR5572 GC15P080662
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ARNT2 on UCSC Golden Path with GeneCards custom track

Promoters for ARNT2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000079924 50 1201 LEF1 MXI1 ZNF76 HIC1 E2F1 ZFHX2 GLIS2 POLR2A PATZ1 SCRT2

Genomic Locations for ARNT2 Gene

Genomic Locations for ARNT2 Gene
193,588 bases
Plus strand

Genomic View for ARNT2 Gene

Genes around ARNT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ARNT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ARNT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ARNT2 Gene

Proteins for ARNT2 Gene

  • Protein details for ARNT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Aryl hydrocarbon receptor nuclear translocator 2
    Protein Accession:
    Secondary Accessions:
    • B4DIS7
    • O15024
    • Q8IYC2

    Protein attributes for ARNT2 Gene

    717 amino acids
    Molecular mass:
    78691 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein (By similarity). Heterodimer with NPAS4 (PubMed:24465693). Heterodimer with the aryl hydrocarbon receptor (AHR) or the SIM1 protein (By similarity). Interacts with TACC3 (By similarity).
    • Sequence=AAH36099.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=BAA20766.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for ARNT2 Gene


neXtProt entry for ARNT2 Gene

Post-translational modifications for ARNT2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ARNT2 Gene

No data available for DME Specific Peptides for ARNT2 Gene

Domains & Families for ARNT2 Gene

Gene Families for ARNT2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for ARNT2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ARNT2: view

No data available for UniProtKB/Swiss-Prot for ARNT2 Gene

Function for ARNT2 Gene

Molecular function for ARNT2 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that plays a role in the development of the hypothalamo-pituitary axis, postnatal brain growth, and visual and renal function (PubMed:24022475). Specifically recognizes the xenobiotic response element (XRE).

Phenotypes From GWAS Catalog for ARNT2 Gene

Gene Ontology (GO) - Molecular Function for ARNT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IDA 24465693
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding ISS,IEA --
genes like me logo Genes that share ontologies with ARNT2: view
genes like me logo Genes that share phenotypes with ARNT2: view

Human Phenotype Ontology for ARNT2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ARNT2 Gene

MGI Knock Outs for ARNT2:

miRNA for ARNT2 Gene

miRTarBase miRNAs that target ARNT2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ARNT2 Gene

Localization for ARNT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ARNT2 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ARNT2 gene
Compartment Confidence
nucleus 5
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ARNT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 12239177
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with ARNT2: view

Pathways & Interactions for ARNT2 Gene

genes like me logo Genes that share pathways with ARNT2: view

Gene Ontology (GO) - Biological Process for ARNT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IDA 12239177
GO:0001701 in utero embryonic development ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA,IDA 11782478
GO:0006366 transcription from RNA polymerase II promoter IEA --
genes like me logo Genes that share ontologies with ARNT2: view

No data available for SIGNOR curated interactions for ARNT2 Gene

Drugs & Compounds for ARNT2 Gene

(1) Drugs for ARNT2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with ARNT2: view

Transcripts for ARNT2 Gene

Unigene Clusters for ARNT2 Gene

Aryl-hydrocarbon receptor nuclear translocator 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ARNT2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b
SP1: - - -
SP2: -
SP4: - -
SP5: -

Relevant External Links for ARNT2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ARNT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ARNT2 Gene

mRNA differential expression in normal tissues according to GTEx for ARNT2 Gene

This gene is overexpressed in Brain - Cortex (x5.1), Brain - Nucleus accumbens (basal ganglia) (x5.0), Brain - Frontal Cortex (BA9) (x4.8), Brain - Anterior cingulate cortex (BA24) (x4.6), Brain - Caudate (basal ganglia) (x4.5), Brain - Amygdala (x4.3), Brain - Putamen (basal ganglia) (x4.2), and Brain - Hippocampus (x4.0).

Protein differential expression in normal tissues from HIPED for ARNT2 Gene

This gene is overexpressed in Monocytes (68.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ARNT2 Gene

Protein tissue co-expression partners for ARNT2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ARNT2 Gene:


SOURCE GeneReport for Unigene cluster for ARNT2 Gene:


Evidence on tissue expression from TISSUES for ARNT2 Gene

  • Nervous system(5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ARNT2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • chin
  • ear
  • eye
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • pituitary gland
  • skull
  • thyroid
  • esophagus
  • heart
  • lung
  • intestine
  • kidney
  • large intestine
  • small intestine
  • stomach
  • pelvis
  • testicle
  • ureter
  • urinary bladder
  • uterus
  • femur
  • hip
  • lower limb
  • thigh
  • blood
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with ARNT2: view

No data available for mRNA Expression by UniProt/SwissProt for ARNT2 Gene

Orthologs for ARNT2 Gene

This gene was present in the common ancestor of animals.

Orthologs for ARNT2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ARNT2 33 34
  • 99.58 (n)
(Bos Taurus)
Mammalia -- 34
  • 97 (a)
ARNT2 33 34
  • 90.75 (n)
(Monodelphis domestica)
Mammalia ARNT2 34
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia ARNT2 34
  • 91 (a)
(Canis familiaris)
Mammalia ARNT2 33 34
  • 90.15 (n)
(Mus musculus)
Mammalia Arnt2 33 16 34
  • 89.04 (n)
(Rattus norvegicus)
Mammalia Arnt2 33
  • 88.86 (n)
(Gallus gallus)
Aves ARNT2 33 34
  • 82.5 (n)
(Anolis carolinensis)
Reptilia ARNT2 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia arnt2 33
  • 77.17 (n)
(Danio rerio)
Actinopterygii arnt2 33 34
  • 75.42 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta tgo 35 34
  • 63 (a)
(Caenorhabditis elegans)
Secernentea aha-1 35 34
  • 48 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2012 34
  • 49 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1118 33
Species where no ortholog for ARNT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ARNT2 Gene

Gene Tree for ARNT2 (if available)
Gene Tree for ARNT2 (if available)

Paralogs for ARNT2 Gene

(4) SIMAP similar genes for ARNT2 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with ARNT2: view

Variants for ARNT2 Gene

Sequence variations from dbSNP and Humsavar for ARNT2 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs1000014841 -- 80,577,417(+) GTGTC(C/T)AACCT intron-variant
rs1000025663 -- 80,538,035(+) GAGCT(A/G)AGTAA intron-variant
rs1000044569 -- 80,433,371(+) ACCTC(G/T)GCCTC intron-variant
rs1000075798 -- 80,433,562(+) CCAAA(G/T)TGCTG intron-variant
rs1000076744 -- 80,595,655(+) GTTTC(A/T)AGAGC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for ARNT2 Gene

Variant ID Type Subtype PubMed ID
nsv570235 CNV loss 21841781
nsv471685 CNV gain 15918152
esv3637019 CNV loss 21293372
esv3581780 CNV loss 25503493
esv3428165 CNV insertion 20981092
esv3382229 CNV insertion 20981092
esv3365028 CNV duplication 20981092
esv2749945 CNV deletion 23290073
esv2004346 CNV deletion 18987734

Variation tolerance for ARNT2 Gene

Residual Variation Intolerance Score: 5.49% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.85; 74.01% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ARNT2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ARNT2 Gene

Disorders for ARNT2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for ARNT2 Gene - From: HGMD, OMIM, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
webb-dattani syndrome
  • hypothalamo-pituitary-frontotemporal hypoplasia with visual and renal anomalies
asperger syndrome
  • asperger disorder
adenoid hypertrophy
  • adenoidal hypertrophy
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards
Search ARNT2 in MalaCards View complete list of genes associated with diseases


  • Webb-Dattani syndrome (WEDAS) [MIM:615926]: A disorder characterized by postnatal microcephaly with fronto-temporal lobe hypoplasia, multiple pituitary hormone deficiency, global developmental delay, seizures, severe visual impairment and abnormalities of the kidneys and urinary tract. {ECO:0000269 PubMed:24022475}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for ARNT2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with ARNT2: view

No data available for Genatlas for ARNT2 Gene

Publications for ARNT2 Gene

  1. Aryl hydrocarbon receptor nuclear translocator 2 (ARNT2): structure, gene mapping, polymorphisms, and candidate evaluation for human orofacial clefts. (PMID: 12210012) Barrow LL … Murray JC (Teratology 2002) 3 4 22 60
  2. Human variants in the neuronal basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) transcription factor complex NPAS4/ARNT2 disrupt function. (PMID: 24465693) Bersten DC … Whitelaw ML (PloS one 2014) 3 4 60
  3. ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies. (PMID: 24022475) Webb EA … Dattani MT (Brain : a journal of neurology 2013) 3 4 60
  4. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 45 60
  5. Genes related to sex steroids, neural growth, and social-emotional behavior are associated with autistic traits, empathy, and Asperger syndrome. (PMID: 19598235) Chakrabarti B … Baron-Cohen S (Autism research : official journal of the International Society for Autism Research 2009) 3 45 60

Products for ARNT2 Gene

Sources for ARNT2 Gene

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