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    VAMP1 vesicle associated membrane protein 1 [ Homo sapiens (human) ]

    Gene ID: 6843, updated on 23-Nov-2023

    Summary

    Official Symbol
    VAMP1provided by HGNC
    Official Full Name
    vesicle associated membrane protein 1provided by HGNC
    Primary source
    HGNC:HGNC:12642
    See related
    Ensembl:ENSG00000139190 MIM:185880; AllianceGenome:HGNC:12642
    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
    SAX1; SYB1; CMS25; SPAX1; VAMP-1
    Summary
    Synapotobrevins, syntaxins, and the 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. Mutations in this gene are associated with autosomal dominant spastic ataxia 1. Multiple alternative splice variants have been described, but the full-length nature of some variants has not been defined. [provided by RefSeq, Jul 2014]
    Expression
    Broad expression in bone marrow (RPKM 21.7), lymph node (RPKM 20.9) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See VAMP1 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6462237..6470677, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6472621..6481015, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6571403..6579843, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene CD27 antisense RNA 1 Neighboring gene SRP14 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6554257-6554758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5858 Neighboring gene CD27 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5861 Neighboring gene TAP binding protein like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4165 Neighboring gene plakophilin 2 pseudogene 1 Neighboring gene mitochondrial ribosomal protein L51

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Myasthenic syndrome, congenital, 25, presynaptic
    MedGen: C5193027 OMIM: 618323 GeneReviews: Not available
    Compare labs
    Spastic ataxia 1
    MedGen: C1970107 OMIM: 108600 GeneReviews: Hereditary Ataxia Overview
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association with bone mass and geometry in the Framingham Heart Study.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp686H12131

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNAP receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in SNARE complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of SNARE complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    NOT located_in azurophil granule membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in mitochondrial outer membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in specific granule membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in synaptic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in tertiary granule membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    vesicle-associated membrane protein 1
    Names
    spastic ataxia 1 (autosomal dominant)
    vesicle-associated membrane protein 1 (synaptobrevin 1)

    NCBI Reference Sequences (RefSeq)

    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_042188.2 RefSeqGene

      Range
      5223..13663
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001297438.2NP_001284367.1  vesicle-associated membrane protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001284367.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1. Isoforms 3 and 4 are the same length but differ in their C-termini.
      Source sequence(s)
      AC005840
      Consensus CDS
      CCDS73422.1
      UniProtKB/TrEMBL
      A8K0D3, F5GZV7
      Related
      ENSP00000444181.1, ENST00000535180.5
      Conserved Domains (1) summary
      cd15870
      Location:3294
      R-SNARE_VAMP2; SNARE motif of VAMP2
    2. NM_014231.5NP_055046.1  vesicle-associated membrane protein 1 isoform 1

      See identical proteins and their annotated locations for NP_055046.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as VAMP-1A, encodes the longest isoform (1).
      Source sequence(s)
      AC005840
      Consensus CDS
      CCDS41740.1
      UniProtKB/Swiss-Prot
      A8MVP3, D3DUR3, O75468, P23763, Q15857, Q6FG94, Q8IVC9
      UniProtKB/TrEMBL
      A8K0D3
      Related
      ENSP00000379602.3, ENST00000396308.4
      Conserved Domains (1) summary
      cd15870
      Location:3294
      R-SNARE_VAMP2; SNARE motif of VAMP2
    3. NM_016830.4NP_058439.1  vesicle-associated membrane protein 1 isoform 3

      See identical proteins and their annotated locations for NP_058439.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), also known as VAMP-1B, contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1. Isoforms 3 and 4 are the same length but differ in their C-termini.
      Source sequence(s)
      AC005840
      Consensus CDS
      CCDS44809.1
      UniProtKB/TrEMBL
      A8K0D3
      Related
      ENSP00000383702.3, ENST00000400911.7
      Conserved Domains (1) summary
      cd15870
      Location:3294
      R-SNARE_VAMP2; SNARE motif of VAMP2
    4. NM_199245.3NP_954740.1  vesicle-associated membrane protein 1 isoform 2

      See identical proteins and their annotated locations for NP_954740.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as VAMP-1D, has a different 3' structure, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC005840
      Consensus CDS
      CCDS31731.1
      UniProtKB/TrEMBL
      A8K0D3
      Related
      ENSP00000355122.3, ENST00000361716.8
      Conserved Domains (1) summary
      cd15870
      Location:3294
      R-SNARE_VAMP2; SNARE motif of VAMP2

    RNA

    1. NR_123717.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate internal exon and contains an alternate 3' terminal exon 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)
      AC005840

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      6462237..6470677 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      6472621..6481015 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)