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Aliases for VAMP1 Gene

Aliases for VAMP1 Gene

  • Vesicle Associated Membrane Protein 1 2 3 5
  • VAMP-1 3 4
  • SYB1 3 4
  • Vesicle-Associated Membrane Protein 1 (Synaptobrevin 1) 3
  • Vesicle-Associated Membrane Protein 1 3
  • Synaptobrevin-1 4
  • Synaptobrevin 1 2
  • SPAX1 3

External Ids for VAMP1 Gene

Previous HGNC Symbols for VAMP1 Gene

  • SYB1

Previous GeneCards Identifiers for VAMP1 Gene

  • GC12M006426
  • GC12M006546
  • GC12M006441
  • GC12M006425
  • GC12M006571

Summaries for VAMP1 Gene

Entrez Gene Summary for VAMP1 Gene

  • 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]

GeneCards Summary for VAMP1 Gene

VAMP1 (Vesicle Associated Membrane Protein 1) is a Protein Coding gene. Diseases associated with VAMP1 include Spastic Ataxia 1, Autosomal Dominant and Presynaptic Congenital Myasthenic Syndromes. Among its related pathways are Uptake and actions of bacterial toxins and Sertoli-Sertoli Cell Junction Dynamics. Gene Ontology (GO) annotations related to this gene include SNARE binding and SNAP receptor activity. An important paralog of this gene is VAMP2.

UniProtKB/Swiss-Prot for VAMP1 Gene

  • Involved in the targeting and/or fusion of transport vesicles to their target membrane.

Gene Wiki entry for VAMP1 Gene

Additional gene information for VAMP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VAMP1 Gene

Genomics for VAMP1 Gene

GeneHancer (GH) Regulatory Elements for VAMP1 Gene

Promoters and enhancers for VAMP1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J006468 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 667.4 +0.7 742 3.1 HDGF PKNOX1 SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 VAMP1 TAPBPL ZNF384 NCAPD2 ENSG00000219410 ENSG00000247853 NOP2 ING4 CHD4 MRPL51
GH12J006472 Enhancer 0.5 ENCODE 650.7 -1.1 -1133 0.2 HDAC2 ZMYM3 BATF E4F1 GC12P006475 VAMP1 MRPL51 CD27-AS1 TAPBPL NCAPD2 SCARNA10 GAPDH ENSG00000255966 CD27
GH12J006530 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 22 -66.1 -66109 12.8 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 GAPDH ENSG00000269968 GPR162 ZNF384 ENSG00000219410 CHD4 ENSG00000247853 NCAPD2 NOP2 SPSB2
GH12J006546 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.8 -80.9 -80928 10.3 HDGF PKNOX1 ARID4B SIN3A YY1 ZNF143 ZNF548 FOS SP3 SP5 IFFO1 CHD4 ENSG00000247853 ENSG00000219410 TAPBPL VAMP1 ZNF384 SCARNA11 SCARNA10 NCAPD2
GH12J006459 Enhancer 1.3 Ensembl ENCODE dbSUPER 32.2 +8.8 8843 6.3 HDGF PKNOX1 ZFP64 IRF4 ZNF213 ZNF207 ZNF143 ATF7 RUNX3 ZNF202 ZNF384 ENSG00000219410 CHD4 ENSG00000247853 TAPBPL MRPL51 NOP2 SCARNA12 VAMP1 ENSG00000126749
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VAMP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VAMP1 gene promoter:
  • c-Myc
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • Max
  • XBP-1
  • ITF-2
  • Tal-1beta
  • AP-1
  • Zic1

Genomic Locations for VAMP1 Gene

Genomic Locations for VAMP1 Gene
8,751 bases
Minus strand
8,751 bases
Minus strand

Genomic View for VAMP1 Gene

Genes around VAMP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VAMP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VAMP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VAMP1 Gene

Proteins for VAMP1 Gene

  • Protein details for VAMP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Vesicle-associated membrane protein 1
    Protein Accession:
    Secondary Accessions:
    • A8MVP3
    • D3DUR3
    • O75468
    • Q15857
    • Q6FG94
    • Q8IVC9

    Protein attributes for VAMP1 Gene

    118 amino acids
    Molecular mass:
    12902 Da
    Quaternary structure:
    • Interacts with VAPA and VAPB.

    Alternative splice isoforms for VAMP1 Gene


neXtProt entry for VAMP1 Gene

Post-translational modifications for VAMP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VAMP1 Gene

No data available for DME Specific Peptides for VAMP1 Gene

Domains & Families for VAMP1 Gene

Gene Families for VAMP1 Gene

Human Protein Atlas (HPA):
  • FDA approved drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for VAMP1 Gene

Suggested Antigen Peptide Sequences for VAMP1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the synaptobrevin family.
  • Belongs to the synaptobrevin family.
genes like me logo Genes that share domains with VAMP1: view

Function for VAMP1 Gene

Molecular function for VAMP1 Gene

UniProtKB/Swiss-Prot Function:
Involved in the targeting and/or fusion of transport vesicles to their target membrane.
GENATLAS Biochemistry:
vesicule associated membrane protein 1,synaptobrevin 1,expressed in neurons,forming a synaptic core complex with syntaxin and synaptosome associated proteins,playing a central role in neural exocytosis,soluble N ethylmaleimide-sensitive factor-attachment protein receptor,SNARE protein

Phenotypes From GWAS Catalog for VAMP1 Gene

Gene Ontology (GO) - Molecular Function for VAMP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA --
GO:0005484 SNAP receptor activity IBA --
GO:0005515 protein binding IPI 9920726
GO:0019905 syntaxin binding IBA --
genes like me logo Genes that share ontologies with VAMP1: view
genes like me logo Genes that share phenotypes with VAMP1: view

Human Phenotype Ontology for VAMP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VAMP1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for VAMP1 Gene

Localization for VAMP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAMP1 Gene

Isoform 1: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass type IV membrane protein. Cell junction, synapse, synaptosome.
Isoform 2: Cytoplasmic vesicle membrane; Single-pass type IV membrane protein. Cell junction, synapse, synaptosome.
Isoform 3: Mitochondrion outer membrane; Single-pass type IV membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VAMP1 gene
Compartment Confidence
plasma membrane 5
mitochondrion 5
cytosol 5
nucleus 1
golgi apparatus 1
endosome 1

Gene Ontology (GO) - Cellular Components for VAMP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005741 mitochondrial outer membrane IEA --
GO:0005829 cytosol TAS --
GO:0005887 integral component of plasma membrane TAS 1976629
GO:0009986 cell surface IEA --
genes like me logo Genes that share ontologies with VAMP1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VAMP1 Gene

Pathways & Interactions for VAMP1 Gene

genes like me logo Genes that share pathways with VAMP1: view

Pathways by source for VAMP1 Gene

1 Qiagen pathway for VAMP1 Gene
1 Cell Signaling Technology pathway for VAMP1 Gene

Gene Ontology (GO) - Biological Process for VAMP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IBA --
GO:0006906 vesicle fusion IBA --
GO:0016192 vesicle-mediated transport IEA --
GO:0035493 SNARE complex assembly IEA --
genes like me logo Genes that share ontologies with VAMP1: view

No data available for SIGNOR curated interactions for VAMP1 Gene

Drugs & Compounds for VAMP1 Gene

(2) Drugs for VAMP1 Gene - From: DrugBank, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Botulinum Toxin Type B Approved, Investigational Pharma binder, Target 0
genes like me logo Genes that share compounds with VAMP1: view

Transcripts for VAMP1 Gene

mRNA/cDNA for VAMP1 Gene

Unigene Clusters for VAMP1 Gene

Vesicle-associated membrane protein 1 (synaptobrevin 1):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VAMP1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VAMP1 Gene

No ASD Table

Relevant External Links for VAMP1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VAMP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VAMP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VAMP1 Gene

This gene is overexpressed in Nasal epithelium (26.6), Frontal cortex (21.8), and Brain (14.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VAMP1 Gene

Protein tissue co-expression partners for VAMP1 Gene

NURSA nuclear receptor signaling pathways regulating expression of VAMP1 Gene:


SOURCE GeneReport for Unigene cluster for VAMP1 Gene:


mRNA Expression by UniProt/SwissProt for VAMP1 Gene:

Tissue specificity: Nervous system, skeletal muscle and adipose tissue.

Evidence on tissue expression from TISSUES for VAMP1 Gene

  • Nervous system(5)
  • Muscle(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VAMP1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • mouth
  • pharynx
  • esophagus
  • stomach
  • foot
  • lower limb
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with VAMP1: view

No data available for mRNA differential expression in normal tissues for VAMP1 Gene

Orthologs for VAMP1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VAMP1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia VAMP1 34 33
  • 99.72 (n)
(Bos Taurus)
Mammalia VAMP1 34
  • 96 (a)
(Mus musculus)
Mammalia Vamp1 16 34 33
  • 93.5 (n)
(Canis familiaris)
Mammalia VAMP1 34 33
  • 92.37 (n)
(Ornithorhynchus anatinus)
Mammalia VAMP1 34
  • 76 (a)
(Gallus gallus)
Aves VAMP1 34 33
  • 79.1 (n)
(Anolis carolinensis)
Reptilia VAMP1 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia vamp1 33
  • 75.19 (n)
(Danio rerio)
Actinopterygii vamp1 34 33
  • 75.85 (n)
VAMP1 (2 of 2) 34
  • 73 (a)
Dr.19773 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10406 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007721 33
  • 64.13 (n)
fruit fly
(Drosophila melanogaster)
Insecta Syb 34 33
  • 59.22 (n)
n-syb 34
  • 33 (a)
(Caenorhabditis elegans)
Secernentea snb-1 34 33
  • 72.37 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SNC1 34
  • 30 (a)
SNC2 34
  • 27 (a)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.14705 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14705 33
Species where no ortholog for VAMP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VAMP1 Gene

Gene Tree for VAMP1 (if available)
Gene Tree for VAMP1 (if available)
Evolutionary constrained regions (ECRs) for VAMP1: view image

Paralogs for VAMP1 Gene

Paralogs for VAMP1 Gene

(5) SIMAP similar genes for VAMP1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with VAMP1: view

Variants for VAMP1 Gene

Sequence variations from dbSNP and Humsavar for VAMP1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs878854975 pathogenic, Ataxia, spastic, 1, autosomal dominant, Spastic paraplegia, not provided 6,464,888(-) A/C coding_sequence_variant, missense_variant, splice_donor_variant
rs71584837 uncertain-significance, not specified 6,462,840(-) G/A 3_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs776075796 uncertain-significance, not specified 6,464,895(-) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs886042861 uncertain-significance, not specified 6,466,289(-) GGGGG/GGGG coding_sequence_variant, frameshift, intron_variant
rs1000101316 -- 6,465,083(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VAMP1 Gene

Variant ID Type Subtype PubMed ID
esv2745471 CNV deletion 23290073
esv2759876 CNV gain 17122850
esv34325 CNV gain 17911159
esv34390 CNV gain 17911159
esv3628406 CNV gain 21293372
nsv1070506 CNV deletion 25765185
nsv442252 CNV gain 18776908
nsv525022 CNV gain 19592680
nsv818881 CNV gain 17921354
nsv8894 CNV gain 18304495

Variation tolerance for VAMP1 Gene

Residual Variation Intolerance Score: 58.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.16; 3.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VAMP1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VAMP1 Gene

Disorders for VAMP1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for VAMP1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spastic ataxia 1, autosomal dominant
  • spax1
presynaptic congenital myasthenic syndromes
  • congenital myasthenic syndromes, presynaptic
spastic ataxia 1
spastic ataxia
  • ataxia, spastic
congenital myasthenic syndrome
  • familial limb-girdle myasthenia
- elite association - COSMIC cancer census association via MalaCards
Search VAMP1 in MalaCards View complete list of genes associated with diseases


  • Spastic ataxia 1, autosomal dominant (SPAX1) [MIM:108600]: An autosomal dominant form of spastic ataxia, a progressive neurodegenerative disorder characterized by lower-limb spasticity and generalized ataxia with dysarthria, impaired ocular movements, and gait disturbance. {ECO:0000269 PubMed:22958904}. Note=The disease is caused by mutations affecting the gene represented in this entry. A mutation affecting a critical donor site for the splicing of VAMP1 isoforms leads to the loss of neuron-specific isoform 1 and subsequently results in haploinsufficiency (PubMed:22958904). Therefore, there would be less neurotransmitter exocytosis in specific regions of the brain, causing the symptoms of SPAX1. {ECO:0000303 PubMed:22958904}.

Additional Disease Information for VAMP1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VAMP1: view

No data available for Genatlas for VAMP1 Gene

Publications for VAMP1 Gene

  1. Structures and chromosomal localizations of two human genes encoding synaptobrevins 1 and 2. (PMID: 1976629) Archer BT … Südhof TC (The Journal of biological chemistry 1990) 2 3 4 22 58
  2. A splice-isoform of vesicle-associated membrane protein-1 (VAMP-1) contains a mitochondrial targeting signal. (PMID: 9658161) Isenmann S … Wattenberg BW (Molecular biology of the cell 1998) 3 4 22 58
  3. VAMP1 mutation causes dominant hereditary spastic ataxia in Newfoundland families. (PMID: 22958904) Bourassa CV … Rouleau GA (American journal of human genetics 2012) 3 4 58
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  5. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PMID: 17903296) Kiel DP … Karasik D (BMC medical genetics 2007) 3 44 58

Products for VAMP1 Gene

Sources for VAMP1 Gene

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