NPAS4 (neuronal PAS domain protein 4)

Gene

• Entrez ID: 266743
• Gene name: Neuronal PAS domain protein 4
• Gene symbol: NPAS4
• Synonyms (NCBI Gene): Le-PAS, NXF, PASD10, bHLHe79
• Chromosome: 11
• Chromosome location: 11q13.2
• Summary: NXF is a member of the basic helix-loop-helix-PER (MIM 602260)-ARNT (MIM 126110)-SIM (see SIM2; MIM 600892) (bHLH-PAS) class of transcriptional regulators, which are involved in a wide range of physiologic and developmental events (Ooe et al., 2004 [PubMe

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2391679	hsa-miR-1224-3p	CLIP-seq
MIRT2391680	hsa-miR-1260	CLIP-seq
MIRT2391681	hsa-miR-1260b	CLIP-seq
MIRT2391682	hsa-miR-1280	CLIP-seq
MIRT2391683	hsa-miR-532-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	14701734
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IDA	24465693
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	14701734
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	24465693
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005667	Component	Transcription regulator complex	IBA
GO:0005667	Component	Transcription regulator complex	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007399	Process	Nervous system development	IEA
GO:0007612	Process	Learning	IEA
GO:0007612	Process	Learning	ISS
GO:0007614	Process	Short-term memory	IEA
GO:0007614	Process	Short-term memory	ISS
GO:0007616	Process	Long-term memory	IEA
GO:0007616	Process	Long-term memory	ISS
GO:0030154	Process	Cell differentiation	IEA
GO:0032228	Process	Regulation of synaptic transmission, GABAergic	IEA
GO:0032228	Process	Regulation of synaptic transmission, GABAergic	ISS
GO:0033554	Process	Cellular response to stress	IEA
GO:0035176	Process	Social behavior	IEA
GO:0035176	Process	Social behavior	ISS
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	14701734, 24465693
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046982	Function	Protein heterodimerization activity	IDA	24465693
GO:0046982	Function	Protein heterodimerization activity	IEA
GO:0046983	Function	Protein dimerization activity	IEA
GO:0048167	Process	Regulation of synaptic plasticity	IEA
GO:0048167	Process	Regulation of synaptic plasticity	ISS
GO:0060079	Process	Excitatory postsynaptic potential	IEA
GO:0060079	Process	Excitatory postsynaptic potential	ISS
GO:0060080	Process	Inhibitory postsynaptic potential	IEA
GO:0060080	Process	Inhibitory postsynaptic potential	ISS
GO:0071386	Process	Cellular response to corticosterone stimulus	IEA
GO:0098794	Component	Postsynapse	IEA
GO:1904862	Process	Inhibitory synapse assembly	IEA
GO:1904862	Process	Inhibitory synapse assembly	ISS

Other IDs

• MIM: 608554
• HGNC: 18983
• e!Ensembl: ENSG00000174576

Protein

• UniProt ID: Q8IUM7
• Protein name: Neuronal PAS domain-containing protein 4 (Neuronal PAS4) (Class E basic helix-loop-helix protein 79) (bHLHe79) (HLH-PAS transcription factor NXF) (PAS domain-containing protein 10)
• Protein function: Transcription factor expressed in neurons of the brain that regulates the excitatory-inhibitory balance within neural circuits and is required for contextual memory in the hippocampus (By similarity). Plays a key role in the structural and funct
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08447	PAS_3	227 → 300	PAS fold	Domain

• Tissue specificity: TISSUE SPECIFICITY: Brain. {ECO:0000269|PubMed:14701734}.
• Sequence:

  MYRSTKGASKARRDQINAEIRNLKELLPLAEADKVRLSYLHIMSLACIYTRKGVFFAGGT
  PLAGPTGLLSAQELEDIVAALPGFLLVFTAEGKLLYLSESVSEHLGHSMVDLVAQGDSIY
  DIIDPADHLTVRQQLTLPSALDTDRLFRCRFNTSKSLRRQSAGNKLVLIRGRFHAHPPGA
  YWAGNPVFTAFCAPLEPRPRPGPGPGPGPASLFLAMFQSRHAKDLALLDISESVLIYLGF
  ERSELLCKSWYGLLHPEDLAHASAQHYRLLAESGDIQAEMVVRLQAKTGGWAWIYCLLYS
  EGPEGPITANNYPISDMEAWSLRQQLNSEDTQAAYVLGTPTMLPSFPENILSQEECSSTN
  PLFTAALGAPRSTSFPSAPELSVVSASEELPRPSKELDFSYLTFPSGPEPSLQAELSKDL
  VCTPPYTPHQPGGCAFLFSLHEPFQTHLPTPSSTLQEQLTPSTATFSDQLTPSSATFPDP
  LTSPLQGQLTETSVRSYEDQLTPCTSTFPDQLLPSTATFPEPLGSPAHEQLTPPSTAFQA
  HLDSPSQTFPEQLSPNPTKTYFAQEGCSFLYEKLPPSPSSPGNGDCTLLALAQLRGPLSV
  DVPLVPEGLLTPEASPVKQSFFHYSEKEQNEIDRLIQQISQLAQGMDRPFSAEAGTGGLE
  PLGGLEPLDSNLSLSGAGPPVLSLDLKPWKCQELDFLADPDNMFLEETPVEDIFMDLSTP
  DPSEEWGSGDPEAEGPGGAPSPCNNLSPEDHSFLEDLATYETAFETGVSAFPYDGFTDEL
  HQLQSQVQDSFHEDGSGGEPTF

• Sequence length: 802

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEPRESSION, BIPOLAR	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOMYELITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anxiety	Anxiety Disorder	BEFREE	27574128		★☆☆☆☆ Found in Text Mining only
Anxiety Disorders	Anxiety Disorder	BEFREE	27574128		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	29556248		★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Cerebral Infarction	BEFREE	26690124		★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	26690124, 27574128		★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognitive disorder	BEFREE	30792384		★☆☆☆☆ Found in Text Mining only
Depression, Bipolar	Bipolar Disorder	PSYGENET_DG	25549857		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Depressive disorder	Mental Depression	BEFREE	29899116		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	33758288	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	29298418, 29899116		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	22030050		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	29222951		★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	22030050	Associate	★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	28416808, 30792384		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	22030050		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	22030050	Associate	★☆☆☆☆ Found in Text Mining only
Ischemic stroke	Ischemic Stroke	BEFREE	26690124		★☆☆☆☆ Found in Text Mining only
Laryngeal Neoplasms	Laryngeal neoplasm	Pubtator	36033826	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29556248		★☆☆☆☆ Found in Text Mining only
Mental Depression	Mental Depression	BEFREE	29899116		★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	22030050		★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic syndrome	Pubtator	36343253	Associate	★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	20977903		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	29899116		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	29915698, 30792384		★☆☆☆☆ Found in Text Mining only
Ovarian Failure, Premature	Ovarian Failure	BEFREE	22030050		★☆☆☆☆ Found in Text Mining only
Premature Menopause	Premature Menopause	BEFREE	22030050		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	PSYGENET_DG	23029555		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	BEFREE	28809400, 30792384		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	33758288	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Status Epilepticus	Status Epilepticus	BEFREE	28128343		★☆☆☆☆ Found in Text Mining only