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FLASH GENE
Symbol VAPB contributors: mct/npt/pgu - updated : 05-01-2016
HGNC name VAMP (vesicle-associated membrane protein)-associated protein B and C
HGNC id 12649
Corresponding disease
ALS8 familial amyotrophic lateral sclerosis 8
SMAPA spinal muscular atrophy proximal, adult type
Location 20q13.32      Physical location : 56.964.244 - 57.021.961
Synonym name
  • VAMP-associated protein B
  • VAMP-associated protein C
  • VAMP-associated 33 kDa protein
  • Synonym symbol(s) VAPC, VAP-B, VAMP-B/VAMP-C, VAP-B/VAP-C
    DNA
    TYPE functioning gene
    STRUCTURE 61.98 kb     6 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status provisional
    Physical map
    RPS4L 20q13.2 ribosomal protein S4-like TFAP2C 20q13.2 transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) PTMAP6 20 prothymosin, alpha pseudogene 6 LOC388800 20 LOC388800 LOC339583 20q13.31 hypothetical LOC339583 BMP7 20q13.2 bone morphogenetic protein 7 (osteogenic protein 1) LOC284754 20q13.31 hypothetical gene supported by BC037891 SPO11 20q13.2-q13.3 SPO11 meiotic protein covalently bound to DSB-like (S. cerevisiae) RAE1 20q13.31 RAE1 RNA export 1 homolog (S. pombe) RNPC1 20q13.31 RNA-binding region (RNP1, RRM) containing 1 LOC149767 20q13.31 similar to dJ579F20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1) CTCFL 20q13.31 CCCTC-binding factor (zinc finger protein)-like PCK1 20q13.3 phosphoenolpyruvate carboxykinase 1 (soluble) ZBP1 17q21.3 Z-DNA binding protein 1 TMEPAI 20q13.31-q13.33 transmembrane, prostate androgen induced RNA C20orf85 20q13.32 chromosome 20 open reading frame 85 C20orf86 20q13.32 chromosome 20 open reading frame 86 PPP4R1L 20q13.32 protein phosphatase 4, regulatory subunit 1-like RAB22A 20q13 RAB22A, member RAS oncogene family VAPB 20q13 VAMP (vesicle-associated membrane protein)-associated protein B and C FLJ90166 20q13.32 hypothetical protein FLJ90166 MGC4294 20q13.32 hypothetical protein MGC4294 LOC388801 20 LOC388801 STX16 20q13.32 syntaxin 16 NPEPL1 20q13.32 aminopeptidase-like 1 LOC388802 20 hypothetical gene supported by AK124059 LOC391258 20 similar to Hypothetical protein KIAA0233 GNAS 20q13.2-q13.3 GNAS complex locus TH1L 20q13 TH1-like (Drosophila) CTSZ 20q13 cathepsin Z TUBB1 20q13.32 tubulin, beta 1 ATP5E 20q13.2-q13.3 ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit C20orf45 20q13.32 chromosome 20 open reading frame 45 MRPS16P 20q13.32 chromosome 20 open reading frame 45 LOC343629 20q13.32 similar to bA379F14.2 (novel protein) C20orf174 20q13.32 chromosome 20 open reading frame 174 EDN3 20q13.2-q13.3 endothelin 3 LOC391259 20 similar to bA164D18.1 (novel protein similar to KIAA0233) SCAPIN1 20q13.32-q13.33 scapinin SYCP2 20q13.33 synaptonemal complex protein 2 PPP1R3D 20q13.3 protein phosphatase 1, regulatory subunit 3D C20orf177 20q13.2-q13.33 chromosome 20 open reading frame 177 CDH26 20q13.2-q13.33 cadherin-like 26 FLJ33860 20q13.33 hypothetical protein FLJ33860 LOC388803 20 LOC388803 LOC388804 20 LOC388804
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    6 - 3689 27.2 243 - 2008 18555774
    3 splicing 1833 11.1 99 - 2010 20227395
  • truncated
  • lacking exons 35,
  • plays an important role in the propagation of hepatitis C virus
  • 3 - 7587 - 99 - 2010 20227395
    VAPB-2
    5 - - - - - 2010 20227395
    lacking exon 3
    4 - - - - - 2010 20227395
    Lacking exons 3-4
    4 - - - - - 2010 20227395
    Lacking exons 4-5
    3 - - - - - 2010 20227395
    Lacking exons 2-3-4
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Endocrineadrenal gland   highly
    Nervousspinal cord   predominantly
    Reproductivefemale systemovary  highly
     male systemprostate   
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumskeletal predominantly
    Nervouscentral   
    cell lineage
    cell lines lymphoma
    fluid/secretion
    at STAGE
    physiological period embryo
    Text
  • expressed early in development in pluripotent stem cells
  • PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • N-terminal MSP (major sperm protein) domain, containing an FFAT-motif binding site (correct distribution of the proline residues would be critical for the correct fold of the MSP domain which is required for recognition of the FFAT motif of its partner), and a VAP consensus sequence (VCS) (
  • a transmembrane domain
  • an amphipathic helical structure
  • a central coiled-coil protein- protein interaction motif
  • a hydrophobic C-terminus acting as a membrane-anchor
  • (endoplasmatic reticulum membrane anchored C-terminal domain)
    mono polymer homomer , heteromer , dimer
    HOMOLOGY
    interspecies homolog to Drosophila DVAP-33A
    homolog to C. elegans VPR-1
    intraspecies homolog to VAPA (60 p100)
    Homologene
    FAMILY
    CATEGORY secretory , signaling
    SUBCELLULAR LOCALIZATION     plasma membrane
        intracellular
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,endoplasmic reticulum
    intracellular,cytoplasm,organelle,Golgi
    intracellular,cytoplasm,organelle,lysosome
    intracellular,cytoplasm,cytosolic,vesicle
    text type IV membrane protein
    basic FUNCTION
  • may be involved in vesicle trafficking
  • playing a a possible role in synaptic homeostasis, by coordinating structural remodeling and post-synaptic sensitivity to neurotransmitter to ensure synaptic efficacy
  • may act as docking sites for cytoplasmic factors to interact with the ER
  • may have structural and regulatory functions based on interactions of the MSP domain
  • plays an important role in the replication of the hepatitis C virus genome
  • can bind to lipid-binding proteins
  • VAPB function is required for transport to the nuclear envelope
  • role of VAPB in tumor promotion in human breast cancer
  • VAPB and the related protein VAPA form homo- and heterodimers that are anchored in the endoplasmic reticulum membrane and can interact with protein partners carrying a FFAT motif
  • is a tail-anchored protein in the endoplasmic reticulum (ER)
  • functions as an adaptor protein to recruit target proteins to the ER and execute various cellular functions, lipid transport, membrane traffic, ER stress
  • binding of VAPB to RAB3GAP1 is implicated in the regulation of nuclear envelope formation through ERGIC
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
  • heterodimer with VAPA
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • interact with VAMP1 and VAMP2
  • interact directly with components of ER homeostatic and stress signaling systems and may therefore be parts of a previously unidentified regulatory pathway (mis-function of such regulatory systems may contribute to the pathological mechanisms of degenerative motor neuron disease)
  • interact with lipid-binding proteins carrying a short motif containing two phenylalanines in an acidic tract (FFAT motif) and targets them to the cytosolic surface of the endoplasmic reticulum (ER)
  • VAPB/ALS8 interacts with FFAT-like proteins including the VCP cofactor FAF1 and the ASNA1 ATPase
  • directly binds to RAB3 GTPase activating protein 1 (RAB3GAP1), the catalytic subunit of RAB3GAP, through the two phenylalanines (FF) in an acidic tract (FFAT)-like motif of RAB3GAP1
  • VAPA, VAPB are endoplasmic reticulum (ER)-resident integral membrane protein that controls a nonvesicular mode of ceramide and cholesterol transfer from the ER to the Golgi complex by interacting with COL4A3BP and oxysterol-binding protein (OSBP), respectively
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) ALS8 , SMAPA
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional     --low  
    reduced levels of VAP family proteins result in decreased ER anchoring of lipid-binding proteins and cause motor neuron degeneration
    constitutional     --low  
    reduced levels of VAPB might be an initial defect leading to ALS8 pathogenesis
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    SystemTypeDisorderPubmed
    neurologyneurodegenerative 
    optimal levels of VAPB may play a central role in the pathogenesis of ALS8, in agreement with the observed reduction of VAPB in sporadic ALS
    ANIMAL & CELL MODELS