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

    Gene ID: 9217, updated on 3-Nov-2024

    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: HPA RNA-seq normal tissues 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. ALS-causing P56S mutation and splicing variation on the hVAPB MSP domain transform its β-sandwich fold into lipid-interacting helical conformations. Qin H, et al. Biochem Biophys Res Commun, 2013 Feb 15. PMID 23333387
    2. A VAPB mutant linked to amyotrophic lateral sclerosis generates a novel form of organized smooth endoplasmic reticulum. Fasana E, et al. FASEB J, 2010 May. PMID 20008544
    3. Structural requirements for VAP-B oligomerization and their implication in amyotrophic lateral sclerosis-associated VAP-B(P56S) neurotoxicity. Kim S, et al. J Biol Chem, 2010 Apr 30. PMID 20207736, Free PMC Article
    4. Novel splice variants of the amyotrophic lateral sclerosis-associated gene VAPB expressed in human tissues. Nachreiner T, et al. Biochem Biophys Res Commun, 2010 Apr 9. PMID 20227395
    5. 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

    See all (248) 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)

    Genotypes

    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 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 
    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 glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_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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    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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