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	VAPA
Symbol Alias	hVAP-33, VAP-A
Approved Name	VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa
Previous Name	VAMP (vesicle-associated membrane protein)-associated protein A (33kD)
Location	18p11.2
Position	chr18:9914002-9960021, 1
External Links	HGNC: 12648 Entrez Gene: 9218 Ensembl: ENSG00000101558 UCSC: uc002koj.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Lohoff, F. W., 2008 (b)	SNP: rs29066, rs29067, rs29145, rs29162, rs29193, rs494015 Haplotype: common haplotypes (ACA ), common haplotypes (CAC ), common haplotypes (AAA ), common haplotypes (CAA ), common haplotypes (AA ), common haplotypes (CC )	Our results provide suggestive evidence of an association between SNPs in the 3' UTR of the VAPA gene and BPD.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 32)

GO terms by PBA (count: 5)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016021	integral component of membrane	cellular component	IEA	219
GO:0004871	signal transducer activity	molecular function	IMP[12761501]	32
GO:0031175	neuron projection development	biological process	IMP[19289470]	10
GO:0019904	protein domain specific binding	molecular function	IPI[20178991]	24
GO:0005886	plasma membrane	cellular component	IDA[10523508]	360

GO terms by database search (count: 27)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007165	signal transduction	biological process	IMP[12761501]	136
GO:0033149	FFAT motif binding	molecular function	IMP[18713837]	1
GO:0005923	tight junction	cellular component	IDA[10523508]	13
GO:0070972	protein localization to endoplasmic reticulum	biological process	IMP[19289470]	2
GO:0015630	microtubule cytoskeleton	cellular component	IEA	12
GO:0031982	vesicle	cellular component	IDA[10523508]	20
GO:0030148	sphingolipid biosynthetic process	biological process	TAS	3
GO:0034975	protein folding in endoplasmic reticulum	biological process	IMP[18713837]	3
GO:0005783	endoplasmic reticulum	cellular component	IDA	49
GO:0070971	endoplasmic reticulum exit site	cellular component	IDA[18713837]	3
GO:0000139	Golgi membrane	cellular component	IMP[18713837]	36
GO:0061025	membrane fusion	biological process	TAS[9657962]	6
GO:0090114	COPII-coated vesicle budding	biological process	IMP[18713837]	1
GO:0008017	microtubule binding	molecular function	IMP[18713837]	10
GO:0044791	positive regulation by host of viral release from host cell	biological process	IDA[19515777]	1
GO:0006665	sphingolipid metabolic process	biological process	TAS	6
GO:0044828	negative regulation by host of viral genome replication	biological process	IDA[19515777]	2
GO:0005789	endoplasmic reticulum membrane	cellular component	TAS	52
GO:0006888	ER to Golgi vesicle-mediated transport	biological process	IMP[18713837]	6
GO:0005515	protein binding	molecular function	IPI[10544080]	563
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	biological process	IMP[12761501]	14
GO:0008219	cell death	biological process	IMP[19289470]	5
GO:0007029	endoplasmic reticulum organization	biological process	IMP[18713837]	3
GO:0046982	protein heterodimerization activity	molecular function	IPI[16227268]	42
GO:0044829	positive regulation by host of viral genome replication	biological process	IDA[19515777]	1
GO:0048471	perinuclear region of cytoplasm	cellular component	IDA[16895911]	50

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04530	Tight junction	18

KEGG pathways by database search (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 4)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
VAPA	SIK1	NO	in vitro	9920726
VAPA	OSBP	NO	in vitro;in vivo;yeast 2-hybrid	12023275
VAPA	NSF	NO	in vitro	11511104
VAPA	VAMP1	NO	in vitro	9657962

Related other genetic factors

Gene related SNPs (count: 18)

Literature-origin SNPs (count: 6)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs29066	chr18:9959638 - 9959638(1)	3_prime_UTR_variant	1(1/0/0)
rs29162	chr18:9931500 - 9931500(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs494015	chr18:9918028 - 9918028(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs29145	chr18:9942078 - 9942078(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs29193	chr18:9924620 - 9924620(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(0/1/0)
rs29067	chr18:9957921 - 9957921(1)	3_prime_UTR_variant; downstream_gene_variant	1(1/0/0)

LD-proxies (count: 12)

rs_ID	Location	Functional Annotation
rs1231581	chr18:9915382 - 9915382(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs636407	chr18:9922515 - 9922515(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs29065	chr18:9961934 - 9961934(1)	downstream_gene_variant
rs683018	chr18:9927115 - 9927115(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs683942	chr18:9926905 - 9926905(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs29129	chr18:9947963 - 9947963(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs29191	chr18:9929333 - 9929333(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs11665575	chr18:9926971 - 9926971(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs11662072	chr18:9947784 - 9947784(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs29206	chr18:9925000 - 9925000(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; splice_region_variant
rs483618	chr18:9963439 - 9963439(1)	downstream_gene_variant
rs3070	chr18:9958525 - 9958525(1)	3_prime_UTR_variant; downstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 5)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
18p11-q12.3	chr18:0-45900000	1 (0/0/1)
18pter-p11	chr18:0-18500000	1 (0/1/0)
Chr 18	chr18:0-80373285	1 (1/0/0)
18p11	chr18:0-18500000	6 (1/2/3)
18p	chr18:0-18500000	1 (0/1/0)

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

Gene relationship with SZ

Gene relationship with MDD

View in gBrowse

Region: chr18:9914002..9960021 View in gBrowse