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Aliases for VAPA Gene

Aliases for VAPA Gene

  • VAMP Associated Protein A 2 3 5
  • VAMP (Vesicle-Associated Membrane Protein)-Associated Protein A, 33kDa 2 3
  • 33 KDa VAMP-Associated Protein 3 4
  • VAMP-A 3 4
  • VAP-33 3 4
  • VAP-A 3 4
  • VAP33 3 4
  • VAMP (Vesicle-Associated Membrane Protein)-Associated Protein A (33kD) 2
  • Vesicle-Associated Membrane Protein-Associated Protein A 3
  • VAMP-Associated Protein A 4
  • HVAP-33 3

External Ids for VAPA Gene

Previous GeneCards Identifiers for VAPA Gene

  • GC18P010047
  • GC18P009903

Summaries for VAPA Gene

Entrez Gene Summary for VAPA Gene

  • 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]

GeneCards Summary for VAPA Gene

VAPA (VAMP Associated Protein A) is a Protein Coding gene. Diseases associated with VAPA include Amyotrophic Lateral Sclerosis 8 and Amyotrophic Lateral Sclerosis Type 14. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics and Metabolism. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and structural molecule activity. An important paralog of this gene is VAPB.

UniProtKB/Swiss-Prot for VAPA Gene

  • Binds to OSBPL3, which mediates recruitment of VAPA to plasma membrane sites (PubMed:25447204). The ORP3-VAPA complex stimulates RRAS signaling which in turn attenuates integrin beta-1 (ITGB1) activation at the cell surface (PubMed:25447204). With OSBPL3, may regulate ER morphology (PubMed:16143324). May play a role in vesicle trafficking (PubMed:11511104, PubMed:19289470).

Gene Wiki entry for VAPA Gene

Additional gene information for VAPA Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VAPA Gene

Genomics for VAPA Gene

GeneHancer (GH) Regulatory Elements for VAPA Gene

Promoters and enhancers for VAPA Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J009912 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 656.2 +2.0 2020 6.3 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 VAPA ENSG00000272799 NAPG TXNDC2 ANKRD12 PPP4R1 RAB31 RNA5SP450
GH18J009823 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.6 -87.5 -87524 6.7 HDGF PKNOX1 ARNT SIN3A YBX1 ZNF766 ZNF207 FOS REST SMARCB1 ANKRD12 VAPA PPP4R1 RAB31 TXNDC2 RALBP1 RN7SL862P ZNF415P1
GH18J009854 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 15.6 -58.6 -58621 2.2 ELF3 FOXA2 MLX RAD21 THRB RARA ZNF614 THAP11 MIXL1 NFKBIZ VAPA TXNDC2 RAB31 PPP4R1 RALBP1 RNA5SP449 PIGPP4
GH18J009848 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.6 -64.1 -64139 2.2 HDGF PKNOX1 ATF1 ARNT ARID2 ZFP91 ATF7 NCOA1 REST ZNF592 RAB31 VAPA TXNDC2 PPP4R1 RNA5SP449 PIGPP4
GH18J009749 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 12.9 -162.0 -161963 5 PKNOX1 FEZF1 RAD21 BRCA1 RFX5 GTF3C2 POLR3A RCOR1 FOS CEBPB PPP4R1 RAB31 ENSG00000263847 VAPA RNU6-903P ANKRD12 ENSG00000266891 GC18M009550
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VAPA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VAPA gene promoter:
  • p53
  • Sp1
  • Max1
  • ATF6
  • GATA-3
  • CREB
  • deltaCREB
  • p300
  • AREB6
  • NF-E2 p45

Genomic Locations for VAPA Gene

Genomic Locations for VAPA Gene
46,064 bases
Plus strand
46,064 bases
Plus strand

Genomic View for VAPA Gene

Genes around VAPA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VAPA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VAPA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VAPA Gene

Proteins for VAPA Gene

  • Protein details for VAPA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Vesicle-associated membrane protein-associated protein A
    Protein Accession:
    Secondary Accessions:
    • A6NDZ0
    • D3DUI3
    • O75453
    • Q5U0E7
    • Q9UBZ2

    Protein attributes for VAPA Gene

    249 amino acids
    Molecular mass:
    27893 Da
    Quaternary structure:
    • Homodimer, and heterodimer with VAPB (PubMed:11511104). Interacts with VAMP1, VAMP2, STX1A, BET1, SEC22C and with the C-terminal domain of OCLN (PubMed:11511104, PubMed:9657962, PubMed:10523508). Interacts with OSBPL1A (By similarity). Interacts (via MSP domain) with ZFYVE27; may retain ZFYVE27 in the endoplasmic reticulum and regulate its function in cell projections formation (PubMed:19289470, PubMed:21976701). Interacts with OSBP (PubMed:20178991). Interacts (via C-terminus) with RSAD2/viperin (via C-terminus) (PubMed:21957124). Interacts with IFITM3 (PubMed:23601107). Interacts with OSBPL3 (phosphorylated form) (PubMed:16143324, PubMed:25447204). Interacts with KIF5A in a ZFYVE27-dependent manner (PubMed:21976701). Interacts with STARD3 (via FFAT motif) (PubMed:24105263). Interacts with STARD3NL (via FFAT motif) (PubMed:24105263).
    • (Microbial infection) Interacts with HCV protein NS5A and NS5B (PubMed:21957124).
    • Sequence=AAD09742.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAF72105.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BG488667; Type=Frameshift; Positions=72, 207, 241; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VAPA Gene

    Alternative splice isoforms for VAPA Gene


neXtProt entry for VAPA Gene

Post-translational modifications for VAPA Gene

  • Ubiquitination at isoforms=2154, isoforms=146, and posLast=1010
  • Modification sites at PhosphoSitePlus

Other Protein References for VAPA Gene

Antibody Products

  • Abcam antibodies for VAPA
  • Boster Bio Antibodies for VAPA
  • Santa Cruz Biotechnology (SCBT) Antibodies for VAPA

No data available for DME Specific Peptides for VAPA Gene

Domains & Families for VAPA Gene

Gene Families for VAPA Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for VAPA Gene

Suggested Antigen Peptide Sequences for VAPA Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the VAMP-associated protein (VAP) (TC 9.B.17) family.
  • Belongs to the VAMP-associated protein (VAP) (TC 9.B.17) family.
genes like me logo Genes that share domains with VAPA: view

Function for VAPA Gene

Molecular function for VAPA Gene

UniProtKB/Swiss-Prot Function:
Binds to OSBPL3, which mediates recruitment of VAPA to plasma membrane sites (PubMed:25447204). The ORP3-VAPA complex stimulates RRAS signaling which in turn attenuates integrin beta-1 (ITGB1) activation at the cell surface (PubMed:25447204). With OSBPL3, may regulate ER morphology (PubMed:16143324). May play a role in vesicle trafficking (PubMed:11511104, PubMed:19289470).

Phenotypes From GWAS Catalog for VAPA Gene

Gene Ontology (GO) - Molecular Function for VAPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 obsolete signal transducer activity HMP --
GO:0005515 protein binding IPI 10544080
GO:0008017 microtubule binding IMP 18713837
GO:0019904 protein domain specific binding IPI 20178991
GO:0033149 FFAT motif binding IMP 18713837
genes like me logo Genes that share ontologies with VAPA: view
genes like me logo Genes that share phenotypes with VAPA: view

Animal Model Products

Clone Products

  • Addgene plasmids for VAPA

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VAPA Gene

Localization for VAPA Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAPA Gene

Endoplasmic reticulum membrane; Single-pass type IV membrane protein. Cell membrane; Single-pass type IV membrane protein. Cell junction, tight junction. Nucleus membrane. Note=Present in the plasma membrane and in intracellular vesicles, together with SNARE proteins. May also associate with the cytoskeleton. Colocalizes with OCLN at the tight junction in polarized epithelial cells. {ECO:0000269 PubMed:10523508}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VAPA gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
lysosome 5
cytoskeleton 3
nucleus 3
cytosol 3
golgi apparatus 3
endosome 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VAPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005634 nucleus IEA --
GO:0005783 endoplasmic reticulum IDA,IEA 18713837
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with VAPA: view

Pathways & Interactions for VAPA Gene

genes like me logo Genes that share pathways with VAPA: view

Pathways by source for VAPA Gene

1 KEGG pathway for VAPA Gene
1 Qiagen pathway for VAPA Gene

Gene Ontology (GO) - Biological Process for VAPA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006888 ER to Golgi vesicle-mediated transport IMP 18713837
GO:0007029 NOT endoplasmic reticulum organization IMP 18713837
GO:0007165 signal transduction IEA --
GO:0008219 cell death IMP 19289470
GO:0030148 sphingolipid biosynthetic process TAS --
genes like me logo Genes that share ontologies with VAPA: view

No data available for SIGNOR curated interactions for VAPA Gene

Drugs & Compounds for VAPA Gene

(2) Drugs for VAPA Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dihydroartemisinin Approved, Investigational Pharma Target, ligand 100

(1) Additional Compounds for VAPA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with VAPA: view

Transcripts for VAPA Gene

Unigene Clusters for VAPA Gene

VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa:
Representative Sequences:

Clone Products

  • Addgene plasmids for VAPA

Alternative Splicing Database (ASD) splice patterns (SP) for VAPA Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d
SP1: - - - - - -
SP2: - - - - -
SP3: - - - - -
SP4: - - -
SP5: - - -
SP6: - - - -
SP8: - - -

Relevant External Links for VAPA Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VAPA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VAPA Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VAPA Gene

Protein tissue co-expression partners for VAPA Gene

NURSA nuclear receptor signaling pathways regulating expression of VAPA Gene:


SOURCE GeneReport for Unigene cluster for VAPA Gene:


mRNA Expression by UniProt/SwissProt for VAPA Gene:

Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for VAPA Gene

  • Nervous system(4.8)
  • Lung(4.7)
  • Liver(4.5)
  • Pancreas(4.5)
  • Adrenal gland(3)
  • Bone marrow(2.6)
  • Eye(2.4)
  • Muscle(2.4)
  • Kidney(2.3)
  • Lymph node(2.3)
  • Spleen(2.2)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with VAPA: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VAPA Gene

Orthologs for VAPA Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VAPA Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia VAPA 34 33
  • 99.77 (n)
(Canis familiaris)
Mammalia VAPA 34 33
  • 94.51 (n)
(Mus musculus)
Mammalia Vapa 16 34 33
  • 93.71 (n)
(Rattus norvegicus)
Mammalia Vapa 33
  • 91.83 (n)
(Ornithorhynchus anatinus)
Mammalia VAPA 34
  • 90 (a)
(Bos Taurus)
Mammalia VAPA 34 33
  • 88.49 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 80 (a)
-- 34
  • 76 (a)
(Gallus gallus)
Aves VAPA 34 33
  • 87.59 (n)
(Anolis carolinensis)
Reptilia VAPA 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia vapa 33
  • 71.66 (n)
Str.6111 33
(Danio rerio)
Actinopterygii vapa 34
  • 85 (a)
vapal 34 33
  • 65.29 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vap-33-1 34 35
  • 35 (a)
fan 34
  • 28 (a)
(Caenorhabditis elegans)
Secernentea vpr-1 34
  • 32 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCS22 34
  • 26 (a)
SCS2 34
  • 24 (a)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.4513 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4513 33
Species where no ortholog for VAPA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VAPA Gene

Gene Tree for VAPA (if available)
Gene Tree for VAPA (if available)
Evolutionary constrained regions (ECRs) for VAPA: view image

Paralogs for VAPA Gene

Paralogs for VAPA Gene

(1) SIMAP similar genes for VAPA Gene using alignment to 2 proteins:

  • J3QKM9_HUMAN Pseudogenes for VAPA Gene

genes like me logo Genes that share paralogs with VAPA: view

Variants for VAPA Gene

Sequence variations from dbSNP and Humsavar for VAPA Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs1000003007 -- 9,922,389(+) C/A genic_upstream_transcript_variant, intron_variant
rs1000026677 -- 9,960,359(+) C/T downstream_transcript_variant
rs1000030035 -- 9,937,328(+) T/C intron_variant
rs1000066664 -- 9,954,841(+) G/C 3_prime_UTR_variant
rs1000097626 -- 9,955,152(+) A/G 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for VAPA Gene

Variant ID Type Subtype PubMed ID
dgv5850n54 CNV loss 21841781
dgv5851n54 CNV gain 21841781
dgv5852n54 CNV gain 21841781
dgv5853n54 CNV gain+loss 21841781
dgv5854n54 CNV gain 21841781
esv1000474 CNV deletion 20482838
esv1026283 CNV deletion 17803354
esv2012315 CNV deletion 18987734
esv24761 CNV loss 19812545
esv2716779 CNV deletion 23290073
esv3641755 CNV gain 21293372
esv3641756 CNV loss 21293372
esv3641757 CNV gain 21293372
esv3641758 CNV loss 21293372
esv3641759 CNV gain 21293372
esv5283 CNV loss 18987735
nsv1056479 CNV gain 25217958
nsv1121535 CNV deletion 24896259
nsv1144826 CNV deletion 24896259
nsv1149629 CNV deletion 26484159
nsv131589 CNV deletion 16902084
nsv131733 CNV deletion 16902084
nsv526637 CNV loss 19592680
nsv527829 CNV gain 19592680
nsv576453 CNV gain 21841781
nsv576457 CNV gain 21841781
nsv576462 CNV gain 21841781
nsv576464 CNV gain 21841781
nsv576465 CNV loss 21841781
nsv833586 CNV loss 17160897
nsv952409 CNV duplication 24416366

Variation tolerance for VAPA Gene

Residual Variation Intolerance Score: 35.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.98; 20.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VAPA Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VAPA Gene

Disorders for VAPA Gene

MalaCards: The human disease database

(6) MalaCards diseases for VAPA Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 8
  • als8
amyotrophic lateral sclerosis type 14
  • amyotrophic lateral sclerosis 14 with or without frontotemporal dementia
  • bronchial pneumonia
infant botulism
  • infant intestinal botulism
visual epilepsy
  • epilepsy, visual
- elite association - COSMIC cancer census association via MalaCards
Search VAPA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VAPA

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VAPA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VAPA Gene

Publications for VAPA Gene

  1. Molecular cloning and characterization of mammalian homologues of vesicle-associated membrane protein-associated (VAMP-associated) proteins. (PMID: 9920726) Nishimura Y … Tanaka T (Biochemical and biophysical research communications 1999) 2 3 4 22 58
  2. Identification of a human homologue of the vesicle-associated membrane protein (VAMP)-associated protein of 33 kDa (VAP-33): a broadly expressed protein that binds to VAMP. (PMID: 9657962) Weir ML … Trimble WS (The Biochemical journal 1998) 2 3 4 22 58
  3. Electrostatic interaction between oxysterol-binding protein and VAMP-associated protein A revealed by NMR and mutagenesis studies. (PMID: 20178991) Furuita K … Kojima C (The Journal of biological chemistry 2010) 3 4 22 58
  4. Promotion of neurite extension by protrudin requires its interaction with vesicle-associated membrane protein-associated protein. (PMID: 19289470) Saita S … Nakayama KI (The Journal of biological chemistry 2009) 3 4 22 58
  5. Association between polymorphisms in the vesicle-associated membrane protein-associated protein A (VAPA) gene on chromosome 18p and bipolar disorder. (PMID: 18665321) Lohoff FW … Berrettini WH (Journal of neural transmission (Vienna, Austria : 1996) 2008) 3 22 44 58

Products for VAPA Gene

Sources for VAPA Gene

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