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VAPB VAMP associated protein B and C [ Homo sapiens (human) ]

Gene ID: 9217, updated on 7-Apr-2025

Summary

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Official Symbol
VAPBprovided by HGNC
Official Full Name
VAMP associated protein B and Cprovided by HGNC
Primary source
HGNC:HGNC:12649
See related
Ensembl:ENSG00000124164 MIM:605704; AllianceGenome:HGNC:12649
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
ALS8; VAP-B; VAMP-B
Summary
The protein encoded by this gene is a type IV membrane protein found in plasma and intracellular vesicle membranes. The encoded protein is found as a homodimer and as a heterodimer with VAPA. This protein also can interact with VAMP1 and VAMP2 and may be involved in vesicle trafficking. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 14.9), brain (RPKM 14.3) and 25 other tissues See more
Orthologs
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Genomic context

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See VAPB in Genome Data Viewer
Location:
20q13.32
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (58389229..58451101)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (60170197..60232150)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56964285..57026157)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:56816520-56817020 Neighboring gene protein phosphatase 4 regulatory subunit 1 like (pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56877500-56878000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13071 Neighboring gene RAB22A, member RAS oncogene family Neighboring gene NANOG hESC enhancer GRCh37_chr20:56947914-56948415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13073 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56988153-56988944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56988945-56989734 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:57002581-57003275 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:57021533-57022034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18173 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:57035877-57036065 Neighboring gene APC down-regulated 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57089058-57090056 Neighboring gene APCDD1L divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:57116639-57117838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57121117-57121618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57134321-57134821 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57169387-57170169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57185055-57185556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57193651-57194322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57194995-57195666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57195667-57196336 Neighboring gene Sharpr-MPRA regulatory region 4326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18176 Neighboring gene long intergenic non-protein coding RNA 1711

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Elimination of the native structure and solubility of the hVAPB MSP domain by the Pro56Ser mutation that causes amyotrophic lateral sclerosis. Shi J, et al. Biochemistry, 2010 May 11. PMID 20377183
  2. Restructured endoplasmic reticulum generated by mutant amyotrophic lateral sclerosis-linked VAPB is cleared by the proteasome. Papiani G, et al. J Cell Sci, 2012 Aug 1. PMID 22611258
  3. A mutation in VAPB that causes amyotrophic lateral sclerosis also causes a nuclear envelope defect. Tran D, et al. J Cell Sci, 2012 Jun 15. PMID 22454507
  4. Amyotrophic lateral sclerosis-associated mutant VAPBP56S perturbs calcium homeostasis to disrupt axonal transport of mitochondria. Mórotz GM, et al. Hum Mol Genet, 2012 May 1. PMID 22258555, Free PMC Article
  5. A novel mutation of VAPB in one Chinese familial amyotrophic lateral sclerosis pedigree and its clinical characteristics. Sun YM, et al. J Neurol, 2017 Dec. PMID 28993872

See all (253) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis.
    Title: Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis.
  2. ARTC1-mediated VAPB ADP-ribosylation regulates calcium homeostasis.
    Title: ARTC1-mediated VAPB ADP-ribosylation regulates calcium homeostasis.
  3. Stimulating VAPB-PTPIP51 ER-mitochondria tethering corrects FTD/ALS mutant TDP43 linked Ca[2+] and synaptic defects.
    Title: Stimulating VAPB-PTPIP51 ER-mitochondria tethering corrects FTD/ALS mutant TDP43 linked Ca(2+) and synaptic defects.
  4. Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.
    Title: Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.
  5. Neurodegeneration-associated protein VAPB regulates proliferation in medulloblastoma.
    Title: Neurodegeneration-associated protein VAPB regulates proliferation in medulloblastoma.
  6. Yeast Models of Amyotrophic Lateral Sclerosis Type 8 Mimic Phenotypes Seen in Mammalian Cells Expressing Mutant VAPB[P56S].
    Title: Yeast Models of Amyotrophic Lateral Sclerosis Type 8 Mimic Phenotypes Seen in Mammalian Cells Expressing Mutant VAPB(P56S).
  7. lncRNA DANCR Promotes Proliferation and Metastasis of Breast Cancer Cells Through Sponging miR-4319 and Upregulating VAPB.
    Title: lncRNA DANCR Promotes Proliferation and Metastasis of Breast Cancer Cells Through Sponging miR-4319 and Upregulating VAPB.
  8. Alteration of Vesicle-Associated Membrane Protein-Binding Protein B in alpha-Synuclein Aggregates in Lewy Body Disease.
    Title: Alteration of Vesicle-Associated Membrane Protein-Binding Protein B in α-Synuclein Aggregates in Lewy Body Disease.
  9. Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3beta.
    Title: Regulating peroxisome-ER contacts via the ACBD5-VAPB tether by FFAT motif phosphorylation and GSK3β.
  10. Sequestosome 1 Is Part of the Interaction Network of VAPB.
    Title: Sequestosome 1 Is Part of the Interaction Network of VAPB.
Submit: New GeneRIF Correction See all GeneRIFs (81)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 FFAT motif binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables beta-tubulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables cadherin binding HDA PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables microtubule binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein 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 IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-membrane adaptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in COPII-coated vesicle budding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in IRE1-mediated unfolded protein response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cholesterol transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in endoplasmic reticulum membrane organization IBA
Inferred from Biological aspect of Ancestor
more info
  
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 unfolded protein response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum-plasma membrane tethering IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in modulation by host of viral RNA genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation by host of viral genome replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation by virus of viral protein levels in host cell 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 viral genome replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to unfolded protein IEA
Inferred from Electronic Annotation
more info
  
involved_in suppression of viral release by host 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 apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
is_active_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in presynapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
vesicle-associated membrane protein-associated protein B/C
Names
VAMP (vesicle-associated membrane protein)-associated protein B and C
VAMP-associated 33 kDa protein

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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.

Genomic

  1. NG_008073.2 RefSeqGene

    Range
    4931..66913
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_656

mRNA and Protein(s)

  1. NM_001195677.2 → NP_001182606.1  vesicle-associated membrane protein-associated protein B/C isoform 2

    See identical proteins and their annotated locations for NP_001182606.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as VAPC and VAMPC) lacks three exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2, also known as VAPC and VAMPC) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AF086629, AK124571, AL035455, BM968517, DA450527
    Consensus CDS
    CCDS56198.1
    UniProtKB/TrEMBL
    Q59EZ6
    Related
    ENSP00000379147.3, ENST00000395802.7
    Conserved Domains (1) summary
    pfam00635
    Location:8 → 90
    Motile_Sperm; MSP (Major sperm protein) domain

  2. NM_004738.5 → NP_004729.1  vesicle-associated membrane protein-associated protein B/C isoform 1

    See identical proteins and their annotated locations for NP_004729.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK023241, AK124571, AL035455, BM968517
    Consensus CDS
    CCDS33498.1
    UniProtKB/Swiss-Prot
    A2A2F2, O95292, O95293, Q9P0H0
    UniProtKB/TrEMBL
    Q53XM7
    Related
    ENSP00000417175.1, ENST00000475243.6
    Conserved Domains (1) summary
    pfam00635
    Location:8 → 111
    Motile_Sperm; MSP (Major sperm protein) domain

RNA

  1. NR_036633.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as VAPB-3,4) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK023241, AK124571, AK298036, AL035455, BM968517, DA450527

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    58389229..58451101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001754433.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    60170197..60232150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008485316.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95292.3 GenPept UniProtKB/Swiss-Prot:O95292

Gene LinkOut

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Chemical Information
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