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    VAMP4 vesicle associated membrane protein 4 [ Homo sapiens (human) ]

    Gene ID: 8674, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VAMP4provided by HGNC
    Official Full Name
    vesicle associated membrane protein 4provided by HGNC
    Primary source
    HGNC:HGNC:12645
    See related
    Ensembl:ENSG00000117533 MIM:606909; AllianceGenome:HGNC:12645
    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
    VAMP-4; VAMP24
    Summary
    Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein SNAP25 are the main components of a protein complex involved in the docking and/or fusion of synaptic vesicles with the presynaptic membrane. The protein encoded by this gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. This protein may play a role in trans-Golgi network-to-endosome transport. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 9.9), testis (RPKM 7.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VAMP4 in Genome Data Viewer
    Location:
    1q24.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (171700160..171742065, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (171056627..171098537, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (171669300..171711205, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene profilin 1 pseudogene 1 Neighboring gene ribosomal protein L4 pseudogene 3 Neighboring gene solute carrier family 5 member 4 pseudogene Neighboring gene solute carrier family 5 member 4 pseudogene

    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. Vesicle-associated membrane protein 4, a positional candidate gene on 1q24-q25, is not associated with type 2 diabetes in the Old Order Amish. Sabra MM, et al. Mol Genet Metab, 2005 Jun. PMID 15896658
    2. Vesicle-associated membrane protein 4 and syntaxin 6 interactions at the chlamydial inclusion. Kabeiseman EJ, et al. Infect Immun, 2013 Sep. PMID 23798538, Free PMC Article
    3. VAMP4 regulates insulin levels by targeting secretory granules to lysosomes. Li M, et al. J Cell Biol, 2022 Oct 3. PMID 36053215, Free PMC Article
    4. Vesicle-associated membrane protein 4 is implicated in trans-Golgi network vesicle trafficking. Steegmaier M, et al. Mol Biol Cell, 1999 Jun. PMID 10359608, Free PMC Article
    5. VAMP4- and VAMP7-expressing vesicles are both required for cytotoxic granule exocytosis in NK cells. Krzewski K, et al. Eur J Immunol, 2011 Nov. PMID 21805468, Free PMC Article

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VAMP4 regulates insulin levels by targeting secretory granules to lysosomes.
      Title: VAMP4 regulates insulin levels by targeting secretory granules to lysosomes.
    2. Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinson's disease.
      Title: Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinson's disease.
    3. Syntaxin 6 and VAMP4 colocalize to the chlamydial inclusion.
      Title: Vesicle-associated membrane protein 4 and syntaxin 6 interactions at the chlamydial inclusion.
    4. CALM is able to sort VAMP4 and VAMP7, even though they have sorting signals for other clathrin adaptors.
      Title: Uncoupling the functions of CALM in VAMP sorting and clathrin-coated pit formation.
    5. Data indicate that depletion of VAMP4, syntaxin 6, syntaxin 16, and Vti1a disrupted the Golgi ribbon structure.
      Title: VAMP4 is required to maintain the ribbon structure of the Golgi apparatus.
    6. colocalization of ATP11B with fluorescent cisplatin and with vesicular trafficking proteins, such as STX6 and VAMP4, strongly suggests that ATP11B contributes to secretory vesicular transport of cisplatin from Golgi to plasma membrane
      Title: ATP11B mediates platinum resistance in ovarian cancer.
    7. The findings of this study suggested that VAMP4 and syb2 diverge functionally, traffic independently and support distinct forms of neurotransmission
      Title: VAMP4 directs synaptic vesicles to a pool that selectively maintains asynchronous neurotransmission.
    8. VAMP7 is involved in many fusion processes and thus plays a more general function in NK-cell activity than VAMP4.
      Title: VAMP4- and VAMP7-expressing vesicles are both required for cytotoxic granule exocytosis in NK cells.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Vesicle-associated membrane protein 4, a positional candidate gene on 1q24-q25, is not associated with type 2 diabetes in the Old Order Amish.
    Submit: New GeneRIF Correction

    Phenotypes

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    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi ribbon formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in SNARE complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in SNARE complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neurotransmitter receptor transport, endosome to postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synaptic vesicle endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic vesicle to endosome fusion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of SNARE complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosome TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in transport vesicle TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    vesicle-associated membrane protein 4
    Names
    VAMP4/TAF3 fusion

    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_001185127.2 → NP_001172056.1  vesicle-associated membrane protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001172056.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
      Source sequence(s)
      BC007019, Z98751
      Consensus CDS
      CCDS53430.1
      UniProtKB/Swiss-Prot
      O75379
      Related
      ENSP00000356714.2, ENST00000367740.2
      Conserved Domains (1) summary
      cd15869
      Location:49 → 115
      R-SNARE_VAMP4; SNARE motif of VAMP4

    2. NM_003762.5 → NP_003753.2  vesicle-associated membrane protein 4 isoform 1

      See identical proteins and their annotated locations for NP_003753.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL035296, DB167275, Z98751
      Consensus CDS
      CCDS1298.1
      UniProtKB/Swiss-Prot
      A2IDD8, O75379, Q96IY9, Q96J20, Q9UEL7
      UniProtKB/TrEMBL
      A0A024R8Z6, Q6IAZ3
      Related
      ENSP00000236192.7, ENST00000236192.12
      Conserved Domains (1) summary
      cd15869
      Location:50 → 116
      R-SNARE_VAMP4; SNARE motif of VAMP4

    RNA

    1. NR_033704.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. This transcript is a candidate for nonsense-mediated mRNA decay is not thought to be translated.
      Source sequence(s)
      AK290441, DB167275, Z98751

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      171700160..171742065 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433375.1 → XP_047289331.1  vesicle-associated membrane protein 4 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      171056627..171098537 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339395.1 → XP_054195370.1  vesicle-associated membrane protein 4 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_201994.1: Suppressed sequence

      Description
      NM_201994.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75379.2 GenPept UniProtKB/Swiss-Prot:O75379

    Gene LinkOut

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

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