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VAPA VAMP associated protein A [ Homo sapiens (human) ]

Gene ID: 9218, updated on 8-Oct-2018

Summary

Official Symbol
VAPAprovided by HGNC
Official Full Name
VAMP associated protein Aprovided by HGNC
Primary source
HGNC:HGNC:12648
See related
Ensembl:ENSG00000101558 MIM:605703; Vega:OTTHUMG00000131603
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VAP-A; VAP33; VAP-33; hVAP-33
Summary
The protein encoded by this gene is a type IV membrane protein. It is present in the plasma membrane and intracellular vesicles. It may also be associated with the cytoskeleton. This protein may function in vesicle trafficking, membrane fusion, protein complex assembly and cell motility. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in adrenal (RPKM 26.8), brain (RPKM 22.1) and 25 other tissues See more
Orthologs

Genomic context

See VAPA in Genome Data Viewer
Location:
18p11.22
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 18 NC_000018.10 (9913958..9960021)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (9913955..9960018)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371982 Neighboring gene thioredoxin domain containing 2 Neighboring gene RNA, 5S ribosomal pseudogene 450 Neighboring gene uncharacterized LOC105371983 Neighboring gene uncharacterized LOC105371984

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with VAMP (vesicle-associated membrane protein)-associated protein A (VAPA) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Diurnally Regulated Genes with Circadian Orthologs, organism-specific biosystem (from WikiPathways)
    Diurnally Regulated Genes with Circadian Orthologs, organism-specific biosystemHuman genes regulated in the diurnal comparison with orthologues that display circadian regulation in mouse heart and liver (Panda 2002, Storch 2002), and SCN (Panda 2002). The 608 significantly regu...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Sphingolipid de novo biosynthesis, organism-specific biosystem (from REACTOME)
    Sphingolipid de novo biosynthesis, organism-specific biosystemThe main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
  • Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
    Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC3745

Gene Ontology Provided by GOA

Function Evidence Code Pubs
FFAT motif binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
cadherin binding HDA PubMed 
microtubule binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
azurophil granule membrane TAS
Traceable Author Statement
more info
 
colocalizes_with bicellular tight junction IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum HDA PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
NOT endoplasmic reticulum exit site IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
microtubule cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vesicle-associated membrane protein-associated protein A
Names
33 kDa VAMP-associated protein
VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa
VAMP-A
epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_003574.5NP_003565.4  vesicle-associated membrane protein-associated protein A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC006238, AF154847, BG488667, BP209270
    Consensus CDS
    CCDS11847.2
    UniProtKB/Swiss-Prot
    Q9P0L0
    Related
    ENSP00000345656.4, OTTHUMP00000162362, ENST00000340541.4, OTTHUMT00000254489
    Conserved Domains (1) summary
    pfam00635
    Location:14118
    Motile_Sperm; MSP (Major sperm protein) domain
  2. NM_194434.2NP_919415.2  vesicle-associated membrane protein-associated protein A isoform 2

    See identical proteins and their annotated locations for NP_919415.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC006238, BC002992, BP209270
    Consensus CDS
    CCDS11848.2
    UniProtKB/Swiss-Prot
    Q9P0L0
    Related
    ENSP00000382880.2, OTTHUMP00000162363, ENST00000400000.6, OTTHUMT00000254490
    Conserved Domains (1) summary
    pfam00635
    Location:14118
    Motile_Sperm; MSP (Major sperm protein) domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p12 Primary Assembly

    Range
    9913958..9960021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451287.1XP_024307055.1  vesicle-associated membrane protein-associated protein A isoform X3

    Conserved Domains (1) summary
    cl27657
    Location:140
    Motile_Sperm; MSP (Major sperm protein) domain
  2. XM_017026079.1XP_016881568.1  vesicle-associated membrane protein-associated protein A isoform X2

  3. XM_011525769.3XP_011524071.1  vesicle-associated membrane protein-associated protein A isoform X1

    Conserved Domains (2) summary
    COG5066
    Location:15199
    SCS2; VAMP-associated protein involved in inositol metabolism [Intracellular trafficking and secretion]
    pfam00635
    Location:20105
    Motile_Sperm; MSP (Major sperm protein) domain
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