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

Gene ID: 9218, updated on 7-Apr-2024

Summary

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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; AllianceGenome:HGNC:12648
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; VAMP-A; 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
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Genomic context

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Location:
18p11.22
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (9914016..9960021)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (10077467..10123397)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (9914013..9960018)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371982 Neighboring gene Sharpr-MPRA regulatory region 4522 Neighboring gene uncharacterized LOC124904245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9290 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:9914515-9915132 Neighboring gene Sharpr-MPRA regulatory region 12110 Neighboring gene RNA, 5S ribosomal pseudogene 450 Neighboring gene NANOG hESC enhancer GRCh37_chr18:9960172-9960690 Neighboring gene uncharacterized LOC124904246 Neighboring gene uncharacterized LOC105371983

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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 Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites. Subra M, et al. Dev Cell, 2023 Jan 23. PMID 36693319
  2. Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR. Furuita K, et al. FEBS Lett, 2021 Sep. PMID 34312846
  3. Circular RNA circVAPA is up-regulated and exerts oncogenic properties by sponging miR-101 in colorectal cancer. Li XN, et al. Biomed Pharmacother, 2019 Apr. PMID 30797148
  4. Association between polymorphisms in the vesicle-associated membrane protein-associated protein A (VAPA) gene on chromosome 18p and bipolar disorder. Lohoff FW, et al. J Neural Transm (Vienna), 2008 Sep. PMID 18665321
  5. Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus. Dorsch AD, et al. Viruses, 2021 Jun 10. PMID 34200728, Free PMC Article

See all (186) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites.
    Title: VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites.
  2. CircVAPA exerts oncogenic property in non-small cell lung cancer by the miR-876-5p/WNT5A axis.
    Title: CircVAPA exerts oncogenic property in non-small cell lung cancer by the miR-876-5p/WNT5A axis.
  3. Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.
    Title: Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.
  4. Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus.
    Title: Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus.
  5. CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
    Title: CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
  6. VAP proteins (VAPs) mediate ER to Golgi tethering and their loss may affect phosphatidylinositol-4-phosphate (PtdIns4P) transfer between these organelles. Loss of VAPs elevates PtdIns4P levels in the Golgi, leading to an expansion of the endosomal pool derived from the Golgi.
    Title: VAMP associated proteins are required for autophagic and lysosomal degradation by promoting a PtdIns4P-mediated endosomal pathway.
  7. Circular RNA VAPA is up-regulated in colorectal cancer and exerts oncogenic properties by sponging miR-101.
    Title: Circular RNA circVAPA is up-regulated and exerts oncogenic properties by sponging miR-101 in colorectal cancer.
  8. Thus, we characterized here MOSPD2, a novel tethering component related to VAP proteins(VAP-A and VAP-B), bridging the endoplasmic reticulum with a variety of distinct organelles.
    Title: Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites.
  9. The silencing of VAP-A or ORP3 abrogated the association of Rab7-positive late endosomes with nuclear envelope invaginations and, hence, the transport of endocytosed EV-derived components to the nucleoplasm of recipient cells.
    Title: VAMP-associated protein-A and oxysterol-binding protein-related protein 3 promote the entry of late endosomes into the nucleoplasmic reticulum.
  10. the component proteins of the machinery, OSBP, VAP, SAC1, and PITPNB, are all essential host factors for AiV replication. Importantly, the machinery is directly recruited to the RNA replication sites through previously unknown interactions of VAP/OSBP/SAC1 with the AiV proteins and with ACBD3.
    Title: Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.
Submit: New GeneRIF Correction See all GeneRIFs (28)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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 PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC3745

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables FFAT motif binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables FFAT motif binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables FFAT motif binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables cadherin binding HDA PubMed 
enables microtubule binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in COPII-coated vesicle budding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ceramide transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cholesterol transport IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in endoplasmic reticulum organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum-plasma membrane tethering IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in membrane fusion TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation by host of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neuron projection development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron projection development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phospholipid transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation by host of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
NOT involved_in protein folding in endoplasmic reticulum IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to endoplasmic reticulum IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sphingomyelin biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sterol transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in viral release from host cell IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in azurophil granule membrane TAS
Traceable Author Statement
more info
  
colocalizes_with bicellular tight junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum HDA PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
NOT located_in endoplasmic reticulum exit site IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in microtubule cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in vesicle IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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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_003574.6 → NP_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, ENST00000340541.4
    Conserved Domains (1) summary
    pfam00635
    Location:14 → 118
    Motile_Sperm; MSP (Major sperm protein) domain

  2. NM_194434.3 → NP_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
    A6NDZ0, D3DUI3, O75453, Q5U0E7, Q9P0L0, Q9UBZ2
    Related
    ENSP00000382880.3, ENST00000400000.7
    Conserved Domains (1) summary
    pfam00635
    Location:14 → 118
    Motile_Sperm; MSP (Major sperm protein) domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    9914016..9960021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437929.1 → XP_047293885.1  vesicle-associated membrane protein-associated protein A isoform X1

  2. XM_047437932.1 → XP_047293888.1  vesicle-associated membrane protein-associated protein A isoform X2

  3. XM_047437930.1 → XP_047293886.1  vesicle-associated membrane protein-associated protein A isoform X1

  4. XM_017026079.2 → XP_016881568.1  vesicle-associated membrane protein-associated protein A isoform X2

  5. XM_047437928.1 → XP_047293884.1  vesicle-associated membrane protein-associated protein A isoform X1

  6. XM_047437931.1 → XP_047293887.1  vesicle-associated membrane protein-associated protein A isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    10077467..10123397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319357.1 → XP_054175332.1  vesicle-associated membrane protein-associated protein A isoform X2

  2. XM_054319359.1 → XP_054175334.1  vesicle-associated membrane protein-associated protein A isoform X2

  3. XM_054319355.1 → XP_054175330.1  vesicle-associated membrane protein-associated protein A isoform X2

  4. XM_054319356.1 → XP_054175331.1  vesicle-associated membrane protein-associated protein A isoform X2

  5. XM_054319353.1 → XP_054175328.1  vesicle-associated membrane protein-associated protein A isoform X1

  6. XM_054319354.1 → XP_054175329.1  vesicle-associated membrane protein-associated protein A isoform X1

  7. XM_054319358.1 → XP_054175333.1  vesicle-associated membrane protein-associated protein A isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P0L0.3 GenPept UniProtKB/Swiss-Prot:Q9P0L0

Gene LinkOut

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