Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	NPAS2
Symbol Alias	MOP4, PASD4, bHLHe9
Approved Name	neuronal PAS domain protein 2
Location	2q11.2
Position	chr2:100820152-100996829, 1
External Links	HGNC: 7895 Entrez Gene: 4862 Ensembl: ENSG00000170485 UCSC: uc002tap.1
No. of Studies	5 (Positive: 3; Negative: 2; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 5)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Kripke, D. F.,2009	SNP: rs1562313	Significant association was observed in the BP group.	Positive	Comment on Study
Mansour, H. A.,2009	SNP: rs11123857, rs13025524, rs17025005, rs6543004	Gene-based tests:X<sup>2</sup>=6.629, P-value = 0.326 in additive model, X<sup>2</sup>=5.686, P-value = 0.553 in dominant model, X<sup>2</sup>=5.077, P-value = 0.701 in recessive model in BPI. Significant association was observed using single SNP-based analyses while no association was observed using gene-based tests in BPI.	Positive	Comment on Study
Soria, V.,2010	SNP: rs11123857, rs11541353, rs13025524, rs13394520, rs17025005, rs17662394, rs2117713, rs3754674, rs4851392, rs7581886	Significant associations of NPAS2 gene were found in BPD patients.	Positive	Comment on Study
Nievergelt, C. M., 2006		Single SNP TDT analyses showed no evidence for association to BPAD.	Negative	Comment on Study
Byrne, E. M., 2014		P-value=0.47. Gene-based tests show no significant association between this gene and BD.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 27)

GO terms by PBA (count: 5)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007417	central nervous system development	biological process	TAS[9012850]	21
GO:0005634	nucleus	cellular component	IDA[14645221]	283
GO:0003700	sequence-specific DNA binding transcription factor activity	molecular function	IEA	66
GO:0004871	signal transducer activity	molecular function	IEA	32
GO:0003677	DNA binding	molecular function	IDA[11441146]; IPI[9576906]	83

GO terms by database search (count: 22)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045475	locomotor rhythm	biological process	IEA	1
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0005667	transcription factor complex	cellular component	IPI[9576906]	18
GO:0045739	positive regulation of DNA repair	biological process	IMP[18819933]	4
GO:0051879	Hsp90 protein binding	molecular function	IDA[9079689]	4
GO:0006974	cellular response to DNA damage stimulus	biological process	IEA	14
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IGI[9576906]	91
GO:0005515	protein binding	molecular function	IPI[14645221]	563
GO:0045893	positive regulation of transcription, DNA-templated	biological process	IDA[11441146]; IMP[18819933]	58
GO:0044255	cellular lipid metabolic process	biological process	TAS	13
GO:2001020	regulation of response to DNA damage stimulus	biological process	IMP[18819933]	2
GO:0006351	transcription, DNA-templated	biological process	IEA	103
GO:0060548	negative regulation of cell death	biological process	IMP[18819933]	5
GO:0046983	protein dimerization activity	molecular function	IEA	19
GO:0001047	core promoter binding	molecular function	ISS	8
GO:0007165	signal transduction	biological process	IEA	136
GO:0042745	circadian sleep/wake cycle	biological process	IEA	2
GO:0007623	circadian rhythm	biological process	TAS	40
GO:0032922	circadian regulation of gene expression	biological process	ISS	22
GO:0046872	metal ion binding	molecular function	IEA	115
GO:0005829	cytosol	cellular component	TAS	223
GO:0051775	response to redox state	biological process	IDA[11441146]	4

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04710	Circadian rhythm	11

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 7)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
NPAS2	NCOA3	NO	in vitro	14645221
NPAS2	HSP90AA1	YES	in vivo	9079689
NPAS2	KAT2B	NO	in vitro	14645221
NPAS2	RXRA	NO	in vitro;yeast 2-hybrid	11439184
NPAS2	ARNTL	YES	in vitro;in vivo;yeast 2-hybrid	11439184 , 9576906
NPAS2	RARA	NO	in vitro;yeast 2-hybrid	11439184
NPAS2	EP300	NO	in vitro;in vivo	14645221

Related other genetic factors

Gene related SNPs (count: 21)

Literature-origin SNPs (count: 12)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs3754674	chr2:100933299 - 100933299(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs1562313	chr2:100970993 - 100970993(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	1(1/0/0)
rs11541353	chr2:100977729 - 100977729(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs7581886	chr2:100964784 - 100964784(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(1/0/0)
rs17025005	chr2:100937152 - 100937152(1)	intron_variant; non_coding_transcript_variant	2(1/1/0)
rs13025524	chr2:100933719 - 100933719(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	2(1/1/0)
rs17662394	chr2:100989274 - 100989274(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(1/0/0)
rs6543004	chr2:100982876 - 100982876(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2117713	chr2:100905505 - 100905505(1)	intron_variant	1(0/1/0)
rs4851392	chr2:100965514 - 100965514(1)	downstream_gene_variant; intron_variant	1(1/0/0)
rs13394520	chr2:100907348 - 100907348(1)	intron_variant	1(0/1/0)
rs11123857	chr2:100987350 - 100987350(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	2(1/1/0)

LD-proxies (count: 9)

rs_ID	Location	Functional Annotation
rs356651	chr2:100925336 - 100925336(1)	intron_variant; non_coding_transcript_variant
rs356656	chr2:100911980 - 100911980(1)	intron_variant
rs356642	chr2:100920976 - 100920976(1)	intron_variant; upstream_gene_variant
rs1621293	chr2:100909202 - 100909202(1)	intron_variant
rs1656306	chr2:100909777 - 100909777(1)	intron_variant
rs10168430	chr2:100904523 - 100904523(1)	intron_variant
rs9679638	chr2:100977992 - 100977992(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2278727	chr2:100982215 - 100982215(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2305160	chr2:100974842 - 100974842(1)	downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
2p16.1-q11.2	chr2:54700000-102100000	1 (1/0/0)
2q11	chr2:93900000-102100000	1 (0/0/1)
Chr 2	chr2:0-242193529	3 (0/3/0)
2p11-q14	chr2:83100000-129100000	1 (0/0/1)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Description	Result Category
19839995	Gene-based tests:X<sup>2</sup>=11.321, P-value = 0.034 in recessive model in SZ/SZA, X<sup>2</sup>=7.892, P-value = 0.205 in dominant model in SZ/SZA, X<sup>2</sup>=5.146, P-value = 0.558 in additive model in SZ/SZA. Nominally significant associations were also noted with the SZ /SZA sample at NPAS2 under a recessive model.Association was observed using both single SNP-based analyses and gene-based tests in SZ/SZA.	Positive
24687905	P-value=0.87. Gene-based tests show no significant association between this gene and SZ.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 1)

Reference	ID in SZGene	Result Category
19839995	884	Positive

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 2)

Reference	Description	Category in MDD
20072116	Significant associations of NPAS2 gene were found in MDD patients.	Positive
24687905	P-value=0.39. Gene-based tests show no significant association between this gene and MDD.	Negative

Overlap with MDD from candidate gene intersection analysis (count: 1)

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Region: chr2:100820152..100996829 View in gBrowse