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

Gene ID: 8674, updated on 3-Nov-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
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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 is implicated in trans-Golgi network vesicle trafficking. Steegmaier M, et al. Mol Biol Cell, 1999 Jun. PMID 10359608, 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. The Di-leucine motif of vesicle-associated membrane protein 4 is required for its localization and AP-1 binding. Peden AA, et al. J Biol Chem, 2001 Dec 28. PMID 11598115
  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 (60) 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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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 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

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