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Aliases for NPAS3 Gene

Aliases for NPAS3 Gene

  • Neuronal PAS Domain Protein 3 2 3 5
  • Class E Basic Helix-Loop-Helix Protein 12 3 4
  • Basic-Helix-Loop-Helix-PAS Protein MOP6 3 4
  • PAS Domain-Containing Protein 6 3 4
  • Member Of PAS Protein 6 3 4
  • Neuronal PAS3 3 4
  • BHLHe12 3 4
  • PASD6 3 4
  • MOP6 3 4

External Ids for NPAS3 Gene

Previous GeneCards Identifiers for NPAS3 Gene

  • GC14P030785
  • GC14P027195
  • GC14P031398
  • GC14P032478
  • GC14P033408
  • GC14P013641

Summaries for NPAS3 Gene

Entrez Gene Summary for NPAS3 Gene

  • This gene encodes a member of the basic helix-loop-helix and PAS domain-containing family of transcription factors. The encoded protein is localized to the nucleus and may regulate genes involved in neurogenesis. Chromosomal abnormalities that affect the coding potential of this gene are associated with schizophrenia and mental retardation. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

GeneCards Summary for NPAS3 Gene

NPAS3 (Neuronal PAS Domain Protein 3) is a Protein Coding gene. Diseases associated with NPAS3 include Learning Disability and Schizophrenia. GO annotations related to this gene include signal transducer activity and protein dimerization activity. An important paralog of this gene is HIF3A.

UniProtKB/Swiss-Prot for NPAS3 Gene

  • May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPAS3 Gene

Genomics for NPAS3 Gene

Regulatory Elements for NPAS3 Gene

Enhancers for NPAS3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around NPAS3 on UCSC Golden Path with GeneCards custom track

Genomic Location for NPAS3 Gene

32,934,909 bp from pter
33,804,176 bp from pter
869,268 bases
Plus strand

Genomic View for NPAS3 Gene

Genes around NPAS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPAS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPAS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPAS3 Gene

Proteins for NPAS3 Gene

  • Protein details for NPAS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuronal PAS domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q86US6
    • Q86US7
    • Q8IXF2
    • Q9BY81
    • Q9H323
    • Q9Y4L8

    Protein attributes for NPAS3 Gene

    933 amino acids
    Molecular mass:
    100805 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein.

    Alternative splice isoforms for NPAS3 Gene

neXtProt entry for NPAS3 Gene

Proteomics data for NPAS3 Gene at MOPED

Post-translational modifications for NPAS3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for NPAS3

No data available for DME Specific Peptides for NPAS3 Gene

Domains & Families for NPAS3 Gene

Gene Families for NPAS3 Gene

Suggested Antigen Peptide Sequences for NPAS3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 bHLH (basic helix-loop-helix) domain.
  • Contains 1 bHLH (basic helix-loop-helix) domain.
  • Contains 1 PAC (PAS-associated C-terminal) domain.
  • Contains 2 PAS (PER-ARNT-SIM) domains.
genes like me logo Genes that share domains with NPAS3: view

Function for NPAS3 Gene

Molecular function for NPAS3 Gene

UniProtKB/Swiss-Prot Function:
May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness (By similarity).

Gene Ontology (GO) - Molecular Function for NPAS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
genes like me logo Genes that share ontologies with NPAS3: view
genes like me logo Genes that share phenotypes with NPAS3: view

Animal Models for NPAS3 Gene

MGI Knock Outs for NPAS3:

Animal Model Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NPAS3 Gene

Localization for NPAS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPAS3 Gene

Subcellular locations from

Jensen Localization Image for NPAS3 Gene COMPARTMENTS Subcellular localization image for NPAS3 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for NPAS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with NPAS3: view

Pathways & Interactions for NPAS3 Gene

SuperPathways for NPAS3 Gene

No Data Available

Interacting Proteins for NPAS3 Gene

Gene Ontology (GO) - Biological Process for NPAS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0032502 developmental process IBA --
genes like me logo Genes that share ontologies with NPAS3: view

No data available for Pathways by source and SIGNOR curated interactions for NPAS3 Gene

Drugs & Compounds for NPAS3 Gene

(1) Additional Compounds for NPAS3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with NPAS3: view

Transcripts for NPAS3 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for NPAS3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - - -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5: -
SP6: -

Relevant External Links for NPAS3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NPAS3 Gene

mRNA expression in normal human tissues for NPAS3 Gene

mRNA differential expression in normal tissues according to GTEx for NPAS3 Gene

This gene is overexpressed in Brain - Amygdala (x5.8), Brain - Nucleus accumbens (basal ganglia) (x4.7), Brain - Caudate (basal ganglia) (x4.3), and Brain - Putamen (basal ganglia) (x4.0).

Protein differential expression in normal tissues from HIPED for NPAS3 Gene

This gene is overexpressed in Pancreatic juice (36.3), Placenta (22.6), and Heart (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NPAS3 Gene

SOURCE GeneReport for Unigene cluster for NPAS3 Gene Hs.657892

mRNA Expression by UniProt/SwissProt for NPAS3 Gene

Tissue specificity: Ubiquitously expressed in the adult brain.
genes like me logo Genes that share expression patterns with NPAS3: view

Protein tissue co-expression partners for NPAS3 Gene

- Elite partner

Primer Products

Orthologs for NPAS3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPAS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia NPAS3 35
  • 93.54 (n)
  • 96.92 (a)
NPAS3 36
  • 94 (a)
(Canis familiaris)
Mammalia NPAS3 35
  • 90.4 (n)
  • 91.38 (a)
NPAS3 36
  • 84 (a)
(Mus musculus)
Mammalia Npas3 35
  • 90.8 (n)
  • 96.36 (a)
Npas3 16
Npas3 36
  • 94 (a)
(Pan troglodytes)
Mammalia NPAS3 35
  • 99.38 (n)
  • 99.35 (a)
NPAS3 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Npas3 35
  • 90.96 (n)
  • 96.07 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 91 (a)
-- 36
  • 90 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 65 (a)
-- 36
  • 99 (a)
(Gallus gallus)
Aves NPAS3 35
  • 82.88 (n)
  • 93.61 (a)
NPAS3 36
  • 91 (a)
(Anolis carolinensis)
Reptilia NPAS3 36
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia npas3 35
  • 72.96 (n)
  • 81.34 (a)
(Danio rerio)
Actinopterygii npas3 35
  • 72.72 (n)
  • 77.73 (a)
NPAS3 36
  • 72 (a)
fruit fly
(Drosophila melanogaster)
Insecta trh 37
  • 45 (a)
trh 36
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3066 36
  • 30 (a)
Species with no ortholog for NPAS3:
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NPAS3 Gene

Gene Tree for NPAS3 (if available)
Gene Tree for NPAS3 (if available)

Paralogs for NPAS3 Gene

Paralogs for NPAS3 Gene

(5) SIMAP similar genes for NPAS3 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with NPAS3: view

Variants for NPAS3 Gene

Sequence variations from dbSNP and Humsavar for NPAS3 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs173383 -- 33,268,277(+) GAATA(C/G)AGACC intron-variant
rs1279198 -- 33,000,886(-) TCCTA(A/G)AATGA intron-variant
rs1279199 -- 32,999,224(-) GGAAT(A/G)TAACA intron-variant
rs1279200 -- 32,997,342(-) tctca(A/T)ctcat intron-variant
rs1279201 -- 32,996,905(-) tccgg(C/G)gtctg intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NPAS3 Gene

Variant ID Type Subtype PubMed ID
esv2536795 CNV Deletion 19546169
esv2131914 CNV Deletion 18987734
esv1461660 CNV Deletion 17803354
esv2673913 CNV Deletion 23128226
nsv526902 CNV Loss 19592680
nsv85863 CNV Loss 16902084
esv2748572 CNV Deletion 23290073
esv2669699 CNV Deletion 23128226
esv28966 CNV Gain 19812545
nsv519095 CNV Gain 19592680
dgv1869n71 CNV Loss 21882294
esv2748573 CNV Deletion 23290073
esv29451 CNV Loss 19812545
esv275082 CNV Gain+Loss 21479260
nsv516217 CNV Gain+Loss 19592680
esv34178 CNV Loss 18971310
nsv832766 CNV Loss 17160897
nsv832767 CNV Gain 17160897
nsv456201 CNV Gain 19166990
esv2662805 CNV Deletion 23128226
esv26657 CNV Loss 19812545
esv271699 CNV Insertion 20981092
esv273707 CNV Insertion 20981092
esv2748575 CNV Deletion 23290073
esv2268114 CNV Deletion 18987734
esv2748576 CNV Deletion 23290073
esv2748577 CNV Deletion 23290073
nsv456202 CNV Loss 19166990
esv268210 CNV Insertion 20981092
esv272661 CNV Insertion 20981092
nsv524579 CNV Loss 19592680
nsv509530 CNV Insertion 20534489
esv274324 CNV Insertion 20981092
nsv507741 CNV Insertion 20534489
nsv515964 CNV Gain 19592680
esv34070 CNV Loss 18971310

Variation tolerance for NPAS3 Gene

Residual Variation Intolerance Score: 16.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.85; 73.98% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NPAS3 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPAS3 Gene

Disorders for NPAS3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NPAS3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
learning disability
  • academic skill disorder
  • schizophrenia 12
- elite association - COSMIC cancer census association via MalaCards
Search NPAS3 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving NPAS3 is found in a family with schizophrenia. Translocation t(9;14)(q34;q13). {ECO:0000269 PubMed:12746393}.

Relevant External Links for NPAS3

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 NPAS3: view

No data available for Genatlas for NPAS3 Gene

Publications for NPAS3 Gene

  1. Disruption of the neuronal PAS3 gene in a family affected with schizophrenia. (PMID: 12746393) Kamnasaran D. … Cox D.W. (J. Med. Genet. 2003) 3 4 23 67
  2. Association of the NPAS3 gene and five other loci with response to the antipsychotic iloperidone identified in a whole genome association study. (PMID: 18521090) Lavedan C. … Polymeropoulos M.H. (Mol. Psychiatry 2009) 3 23
  3. Genome-wide pharmacogenomic analysis of the response to interferon beta therapy in multiple sclerosis. (PMID: 18195134) Byun E. … Oksenberg J.R. (Arch. Neurol. 2008) 3 23
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3
  5. A mutation in NPAS3 segregates with mental illness in a small family. (PMID: 23337948) Yu L. … Nucifora F.C. (Mol. Psychiatry 2014) 3

Products for NPAS3 Gene

Sources for NPAS3 Gene