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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
  • Neuronal PAS Domain-Containing Protein 3 3
  • BHLHE12 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 cognitive disability. 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 Holoprosencephaly 8 and Schizophrenia. Gene Ontology (GO) annotations related to this gene include obsolete signal transducer activity and protein dimerization activity. An important paralog of this gene is NPAS1.

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).

Additional gene information for NPAS3 Gene

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

Genomics for NPAS3 Gene

GeneHancer (GH) Regulatory Elements for NPAS3 Gene

Promoters and enhancers for NPAS3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J032937 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 650.7 +4.4 4438 2.8 PKNOX1 MZF1 RAD21 ZNF335 GLIS2 ZNF366 SCRT2 ZNF202 SP3 ZNF398 NPAS3 GC14M032964
GH14J032932 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE 652.6 -1.2 -1174 2.5 ZSCAN4 INSM2 KLF17 FEZF1 GLI4 ZNF2 ZNF335 GLIS2 ZNF366 ZNF143 NPAS3 ENSG00000280281
GH14J032200 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.2 -732.5 -732515 4.1 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 SP3 AKAP6 GC14P032203 RNU6-7 RNU6-8 HECTD1 LOC100533787 ENSG00000257472 ENSG00000257155 ENSG00000258196 NPAS3
GH14J032134 Enhancer 1 ENCODE 14.8 -800.0 -800049 0.1 PKNOX1 CLOCK ARNT ZNF133 NEUROD1 FEZF1 GLI4 ZNF2 YY1 ZNF121 ARHGAP5 RNU6-8 NPAS3 LOC100533787 ENSG00000257472 ENSG00000257155 ENSG00000258196 RNU6-7 HECTD1 DTD2
GH14J032506 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 6.7 -425.8 -425819 4.7 FOXA2 SIN3A BRCA1 RFX5 YY1 ATF7 RXRA CEBPB ZEB2 REST AKAP6 NPAS3 ARHGAP5 MTCO1P2 GC14P032628
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPAS3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NPAS3 gene promoter:
  • NRSF form 2
  • NRSF form 1
  • CUTL1
  • E47
  • Tal-1beta
  • GATA-3
  • MyoD
  • ARP-1

Genomic Locations for NPAS3 Gene

Genomic Locations for NPAS3 Gene
869,268 bases
Plus strand
869,244 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

Post-translational modifications for NPAS3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NPAS3 Gene

Domains & Families for NPAS3 Gene

Gene Families for NPAS3 Gene

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

Suggested Antigen Peptide Sequences for NPAS3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for NPAS3 Gene

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).

Phenotypes From GWAS Catalog for NPAS3 Gene

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 ISM 19274049
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IEA --
GO:0046983 protein dimerization activity IEA --
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

Clone 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

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 NPAS3 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NPAS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with NPAS3: view

Pathways & Interactions for NPAS3 Gene

SuperPathways for NPAS3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NPAS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0032502 developmental process IBA --
GO:0045893 positive regulation of transcription, DNA-templated ISS --
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) Drugs for NPAS3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with NPAS3: view

Transcripts for NPAS3 Gene

Unigene Clusters for NPAS3 Gene

Neuronal PAS domain protein 3:
Representative Sequences:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for NPAS3 Gene

Protein tissue co-expression partners for NPAS3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NPAS3 Gene:


SOURCE GeneReport for Unigene cluster for NPAS3 Gene:


mRNA Expression by UniProt/SwissProt for NPAS3 Gene:

Tissue specificity: Ubiquitously expressed in the adult brain.

Evidence on tissue expression from TISSUES for NPAS3 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with NPAS3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NPAS3 Gene

Orthologs for NPAS3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPAS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NPAS3 34 33
  • 99.38 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 99 (a)
-- 34
  • 65 (a)
(Bos Taurus)
Mammalia NPAS3 34 33
  • 93.54 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 91 (a)
-- 34
  • 90 (a)
(Rattus norvegicus)
Mammalia Npas3 33
  • 90.96 (n)
(Mus musculus)
Mammalia Npas3 16 34 33
  • 90.8 (n)
(Canis familiaris)
Mammalia NPAS3 34 33
  • 90.4 (n)
(Gallus gallus)
Aves NPAS3 34 33
  • 82.88 (n)
(Anolis carolinensis)
Reptilia NPAS3 34
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia npas3 33
  • 72.96 (n)
(Danio rerio)
Actinopterygii npas3 33
  • 72.72 (n)
NPAS3 34
  • 72 (a)
fruit fly
(Drosophila melanogaster)
Insecta trh 34 35
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3066 34
  • 30 (a)
Species where no ortholog for NPAS3 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)
  • worm (Caenorhabditis elegans)

Evolution for NPAS3 Gene

Gene Tree for NPAS3 (if available)
Gene Tree for NPAS3 (if available)
Evolutionary constrained regions (ECRs) for NPAS3: view image

Paralogs for NPAS3 Gene

Paralogs for NPAS3 Gene

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

  • F8VR32_HUMAN
  • F8VS42_HUMAN
  • F8W0C2_HUMAN
  • H0YI42_HUMAN
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 Variation AA Info Type
rs1000001865 -- 33,527,935(+) G/A intron_variant
rs1000002420 -- 33,021,043(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000003520 -- 33,309,837(+) G/A intron_variant
rs1000004943 -- 33,736,236(+) A/G intron_variant
rs1000005566 -- 33,696,815(+) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
dgv1864n100 CNV loss 25217958
esv1461660 CNV deletion 17803354
esv2131914 CNV deletion 18987734
esv2268114 CNV deletion 18987734
esv2536795 CNV deletion 19546169
esv2662805 CNV deletion 23128226
esv26657 CNV loss 19812545
esv2669699 CNV deletion 23128226
esv2673913 CNV deletion 23128226
esv2748572 CNV deletion 23290073
esv2748573 CNV deletion 23290073
esv2748575 CNV deletion 23290073
esv2748576 CNV deletion 23290073
esv2748577 CNV deletion 23290073
esv275082 CNV gain+loss 21479260
esv28966 CNV gain 19812545
esv29451 CNV loss 19812545
esv3303931 CNV mobile element insertion 20981092
esv3308388 CNV mobile element insertion 20981092
esv3309435 CNV mobile element insertion 20981092
esv3310052 CNV mobile element insertion 20981092
esv3352327 CNV insertion 20981092
esv3394834 CNV insertion 20981092
esv3406701 CNV insertion 20981092
esv34070 CNV loss 18971310
esv34178 CNV loss 18971310
esv3423566 CNV insertion 20981092
esv3451142 CNV insertion 20981092
esv3551346 CNV deletion 23714750
esv3581109 CNV loss 25503493
esv3584664 CNV loss 24956385
esv3633998 CNV loss 21293372
esv3633999 CNV loss 21293372
esv3634000 CNV loss 21293372
esv3634001 CNV loss 21293372
esv3634004 CNV loss 21293372
esv3634005 CNV loss 21293372
esv3634010 CNV loss 21293372
esv3634014 CNV gain 21293372
esv3892498 CNV loss 25118596
nsv1035564 CNV loss 25217958
nsv1036028 CNV loss 25217958
nsv1037356 CNV loss 25217958
nsv1054534 CNV loss 25217958
nsv1069789 CNV deletion 25765185
nsv1111100 CNV tandem duplication 24896259
nsv1111101 CNV tandem duplication 24896259
nsv1121873 CNV deletion 24896259
nsv1126362 CNV deletion 24896259
nsv1128694 CNV duplication 24896259
nsv1144715 CNV deletion 24896259
nsv1150421 CNV deletion 26484159
nsv456201 CNV gain 19166990
nsv456202 CNV loss 19166990
nsv507741 OTHER sequence alteration 20534489
nsv509530 CNV insertion 20534489
nsv515964 CNV gain 19592680
nsv516217 CNV gain+loss 19592680
nsv519095 CNV gain 19592680
nsv524579 CNV loss 19592680
nsv526902 CNV loss 19592680
nsv564186 CNV loss 21841781
nsv564187 CNV loss 21841781
nsv564188 CNV loss 21841781
nsv564189 CNV gain 21841781
nsv564190 CNV loss 21841781
nsv564191 CNV loss 21841781
nsv832766 CNV loss 17160897
nsv832767 CNV gain 17160897
nsv85863 CNV deletion 16902084

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)

Additional Variant Information for NPAS3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NPAS3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
holoprosencephaly 8
  • hpe8
  • sczd
learning disability
  • academic skill disorder
  • holoprosencephaly sequence
- 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}.

Additional Disease Information for NPAS3

Genetic Association Database
Human Genome Epidemiology 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. 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 MH (Molecular psychiatry 2009) 3 22 44 58
  2. Disruption of the neuronal PAS3 gene in a family affected with schizophrenia. (PMID: 12746393) Kamnasaran D … Cox DW (Journal of medical genetics 2003) 3 4 22 58
  3. A genome-wide association study of inflammatory biomarker changes in response to fenofibrate treatment in the Genetics of Lipid Lowering Drug and Diet Network. (PMID: 22228203) Aslibekyan S … Arnett DK (Pharmacogenetics and genomics 2012) 3 44 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for NPAS3 Gene

Sources for NPAS3 Gene

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