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Aliases for VAMP4 Gene

Aliases for VAMP4 Gene

  • Vesicle Associated Membrane Protein 4 2 3 5
  • VAMP-4 3 4
  • Vesicle-Associated Membrane Protein 4 3
  • VAMP4/TAF3 Fusion 3
  • VAMP24 3

External Ids for VAMP4 Gene

Previous GeneCards Identifiers for VAMP4 Gene

  • GC01M169237
  • GC01M167298
  • GC01M168250
  • GC01M168908
  • GC01M168400
  • GC01M169935
  • GC01M171669
  • GC01M142893

Summaries for VAMP4 Gene

Entrez Gene Summary for VAMP4 Gene

  • 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]

GeneCards Summary for VAMP4 Gene

VAMP4 (Vesicle Associated Membrane Protein 4) is a Protein Coding gene. Diseases associated with VAMP4 include Mental Retardation, Enteropathy, Deafness, Peripheral Neuropathy, Ichthyosis, And Keratoderma and Human Granulocytic Anaplasmosis. Among its related pathways are Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics and Clathrin-mediated endocytosis. Gene Ontology (GO) annotations related to this gene include SNARE binding and SNAP receptor activity. An important paralog of this gene is ENSG00000263620.

UniProtKB/Swiss-Prot for VAMP4 Gene

  • Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for this sorting pathway that is critical for remodeling the secretory response of granule.

Gene Wiki entry for VAMP4 Gene

Additional gene information for VAMP4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VAMP4 Gene

Genomics for VAMP4 Gene

GeneHancer (GH) Regulatory Elements for VAMP4 Gene

Promoters and enhancers for VAMP4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J171738 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 659.3 +0.8 818 6.2 ZFP64 DMAP1 IRF4 YY1 ZNF213 ZNF143 SP3 ZNF610 GLIS1 NBN VAMP4 PRRC2C METTL13 PIGC FMO4 SUCO MYOC PIR43253
GH01J171753 Enhancer 1.1 Ensembl ENCODE dbSUPER 8.4 -12.4 -12425 2 PKNOX1 TAF9B NFIB ZBTB40 E4F1 CBX5 NCOR1 FOXK2 ZSCAN29 NANOG LOC100422549 METTL13 MYOC VAMP4 LOC100422548
GH01J171652 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 5.2 +87.2 87210 5.6 PKNOX1 FOXA2 RB1 ARNT ZNF2 RAD21 RARA YY1 SCRT2 ZNF143 MYOC VAMP4 PFN1P1 GC01P171514
GH01J171744 Enhancer 0.8 FANTOM5 Ensembl dbSUPER 10.2 -2.9 -2877 0.6 ZBTB33 MYOC METTL13 VAMP4 FMO4 PRRC2C LOC100422548
GH01J171644 Enhancer 1.3 Ensembl ENCODE dbSUPER 5.7 +96.5 96545 1.8 HDGF PKNOX1 ATF1 ARID4B ZNF2 IRF4 ZNF48 YY1 GTF3C2 ARID2 PRRC2C METTL13 PIGC MYOC VAMP4 GC01P171602 GC01P171514
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VAMP4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VAMP4 gene promoter:
  • AP-1
  • c-Jun
  • ATF-2
  • Pax-5
  • NF-kappaB
  • NF-kappaB1
  • RelA
  • LyF-1
  • FOXJ2 (long isoform)
  • FOXJ2

Genomic Locations for VAMP4 Gene

Genomic Locations for VAMP4 Gene
chr1:171,700,156-171,742,247
(GRCh38/hg38)
Size:
42,092 bases
Orientation:
Minus strand
chr1:171,669,296-171,711,387
(GRCh37/hg19)
Size:
42,092 bases
Orientation:
Minus strand

Genomic View for VAMP4 Gene

Genes around VAMP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VAMP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VAMP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VAMP4 Gene

Proteins for VAMP4 Gene

  • Protein details for VAMP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75379-VAMP4_HUMAN
    Recommended name:
    Vesicle-associated membrane protein 4
    Protein Accession:
    O75379
    Secondary Accessions:
    • A2IDD8
    • Q96IY9
    • Q96J20
    • Q9UEL7

    Protein attributes for VAMP4 Gene

    Size:
    141 amino acids
    Molecular mass:
    16397 Da
    Quaternary structure:
    • Identified in a complex containing STX6, STX12, VAMP4 and VTI1A (By similarity). Interacts with BAIAP3; this interaction is increased in the presence of calcium (PubMed:28626000).

    Alternative splice isoforms for VAMP4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VAMP4 Gene

Post-translational modifications for VAMP4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VAMP4 Gene

No data available for DME Specific Peptides for VAMP4 Gene

Domains & Families for VAMP4 Gene

Gene Families for VAMP4 Gene

Protein Domains for VAMP4 Gene

Graphical View of Domain Structure for InterPro Entry

O75379

UniProtKB/Swiss-Prot:

VAMP4_HUMAN :
  • Belongs to the synaptobrevin family.
Family:
  • Belongs to the synaptobrevin family.
genes like me logo Genes that share domains with VAMP4: view

Function for VAMP4 Gene

Molecular function for VAMP4 Gene

UniProtKB/Swiss-Prot Function:
Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for this sorting pathway that is critical for remodeling the secretory response of granule.

Phenotypes From GWAS Catalog for VAMP4 Gene

Gene Ontology (GO) - Molecular Function for VAMP4 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 16189514
genes like me logo Genes that share ontologies with VAMP4: view
genes like me logo Genes that share phenotypes with VAMP4: view

Animal Model Products

  • Taconic Biosciences Mouse Models for VAMP4

Clone Products

  • Addgene plasmids for VAMP4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VAMP4 Gene

Localization for VAMP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VAMP4 Gene

Golgi apparatus, trans-Golgi network membrane; Single-pass type IV membrane protein. Note=Associated with trans Golgi network (TGN) and newly formed immature secretory granules (ISG). Not found on the mature secretory organelles.

Subcellular locations from

COMPARTMENTS
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 VAMP4 gene
Compartment Confidence
plasma membrane 5
golgi apparatus 5
endosome 5
lysosome 4
cytosol 3
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VAMP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS 9553086
GO:0005764 lysosome TAS 9553086
GO:0005768 endosome TAS 9553086
GO:0005794 Golgi apparatus IDA,IEA 23677696
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with VAMP4: view

Pathways & Interactions for VAMP4 Gene

genes like me logo Genes that share pathways with VAMP4: view

SIGNOR curated interactions for VAMP4 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for VAMP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000226 microtubule cytoskeleton organization IMP 23677696
GO:0006887 exocytosis IBA --
GO:0006888 NOT ER to Golgi vesicle-mediated transport IMP 23677696
GO:0006906 vesicle fusion IBA --
GO:0016192 vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with VAMP4: view

Drugs & Compounds for VAMP4 Gene

(1) Drugs for VAMP4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with VAMP4: view

Transcripts for VAMP4 Gene

mRNA/cDNA for VAMP4 Gene

Unigene Clusters for VAMP4 Gene

Vesicle-associated membrane protein 4:
Representative Sequences:

Clone Products

  • Addgene plasmids for VAMP4

Alternative Splicing Database (ASD) splice patterns (SP) for VAMP4 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c · 9d ^ 10a · 10b
SP1: - - - - - - -
SP2: - - - -
SP3: - - - -
SP4: -
SP5: - -
SP6: - - -
SP7:

Relevant External Links for VAMP4 Gene

GeneLoc Exon Structure for
VAMP4
ECgene alternative splicing isoforms for
VAMP4

Expression for VAMP4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VAMP4 Gene

Protein differential expression in normal tissues from HIPED for VAMP4 Gene

This gene is overexpressed in Bone (26.9), Pancreas (7.2), Liver (6.5), and Fetal Brain (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VAMP4 Gene



Protein tissue co-expression partners for VAMP4 Gene

NURSA nuclear receptor signaling pathways regulating expression of VAMP4 Gene:

VAMP4

SOURCE GeneReport for Unigene cluster for VAMP4 Gene:

Hs.6651

Evidence on tissue expression from TISSUES for VAMP4 Gene

  • Bone marrow(4.2)
  • Liver(4.2)
  • Nervous system(3.7)
genes like me logo Genes that share expression patterns with VAMP4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VAMP4 Gene

Orthologs for VAMP4 Gene

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

Orthologs for VAMP4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VAMP4 34 33
  • 100 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VAMP4 34 33
  • 96.93 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VAMP4 34
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vamp4 16 34 33
  • 94.72 (n)
rat
(Rattus norvegicus)
Mammalia Vamp4 33
  • 94.17 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 94 (a)
OneToMany
-- 34
  • 94 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia VAMP4 34
  • 91 (a)
OneToOne
chicken
(Gallus gallus)
Aves VAMP4 34 33
  • 78.72 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VAMP4 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vamp4 33
  • 77.07 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12760 33
zebrafish
(Danio rerio)
Actinopterygii vamp4 34 33
  • 71.19 (n)
OneToOne
zgc73166 33
worm
(Caenorhabditis elegans)
Secernentea snb-2 34
  • 28 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SNC2 36 34
  • 30 (a)
SNC1 34
  • 30 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea Cin.5545 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5545 33
Species where no ortholog for VAMP4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 VAMP4 Gene

ENSEMBL:
Gene Tree for VAMP4 (if available)
TreeFam:
Gene Tree for VAMP4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VAMP4: view image

Paralogs for VAMP4 Gene

Paralogs for VAMP4 Gene

(7) SIMAP similar genes for VAMP4 Gene using alignment to 2 proteins:

  • VAMP4_HUMAN
  • Q6IAZ3_HUMAN
genes like me logo Genes that share paralogs with VAMP4: view

Variants for VAMP4 Gene

Sequence variations from dbSNP and Humsavar for VAMP4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000040510 -- 171,719,639(-) A/G intron_variant
rs1000078816 -- 171,742,021(-) G/T 5_prime_UTR_variant, non_coding_transcript_variant
rs1000147804 -- 171,724,879(-) A/G intron_variant
rs1000183833 -- 171,711,908(-) T/C intron_variant
rs1000236190 -- 171,711,599(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VAMP4 Gene

Variant ID Type Subtype PubMed ID
esv2719529 CNV deletion 23290073
esv28731 CNV gain+loss 19812545
nsv3509 CNV insertion 18451855

Variation tolerance for VAMP4 Gene

Residual Variation Intolerance Score: 51.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.61; 13.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VAMP4 Gene

Human Gene Mutation Database (HGMD)
VAMP4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VAMP4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VAMP4 Gene

Disorders for VAMP4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VAMP4 Gene - From: HGMD and DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search VAMP4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VAMP4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VAMP4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VAMP4 Gene

Publications for VAMP4 Gene

  1. Seven novel mammalian SNARE proteins localize to distinct membrane compartments. (PMID: 9553086) Advani RJ … Scheller RH (The Journal of biological chemistry 1998) 2 3 4 58
  2. BAIAP3, a C2 domain-containing Munc13 protein, controls the fate of dense-core vesicles in neuroendocrine cells. (PMID: 28626000) Zhang X … Martin TFJ (The Journal of cell biology 2017) 3 4 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  4. Vesicle-associated membrane protein 4, a positional candidate gene on 1q24-q25, is not associated with type 2 diabetes in the Old Order Amish. (PMID: 15896658) Sabra MM … Shuldiner AR (Molecular genetics and metabolism 2005) 3 44 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for VAMP4 Gene

Sources for VAMP4 Gene

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