VAMP3 Gene

HGNC Family	Vesicle-associated membrane proteins (VAMP)
Name	vesicle-associated membrane protein 3
Description	Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein are the main components of a protein complex involved in the docking and/or fusion of synaptic vesicles with the presynaptic membrane. This gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. Because of its high homology to other known VAMPs, its broad tissue distribution, and its subcellular localization, the protein encoded by this gene was shown to be the human equivalent of the rodent cellubrevin. In platelets the protein resides on a compartment that is not mobilized to the plasma membrane on calcium or thrombin stimulation. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nVAMP3 is an essential R‐SNARE protein that mediates key vesicular fusion events underlying intracellular trafficking. It is required for the fusion between multivesicular bodies and autophagosomes to form amphisomes, a process critical for autophagosome maturation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " In addition, VAMP3 facilitates the delivery of matrix metalloproteinases—such as MMP2 and MMP9—to the plasma membrane to promote extracellular matrix remodeling"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": ", and it governs the recycling of key adhesion receptors like integrins, thereby impacting cell adhesion and chemotactic migration."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": " Moreover, its dynamic trafficking is modulated by interactions with phosphatidylinositol 4-phosphate—mediated by PI4K2A"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "—and by ubiquitylation events that further control recycling endosome pathways."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn secretion processes, VAMP3 plays pivotal roles in regulated exocytosis across diverse cell types. It contributes to platelet granule release, where its perturbation affects both alpha- and dense-granule secretion"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": ", and it mediates the Ca²⁺-triggered fusion of Weibel-Palade bodies in endothelial cells, ensuring efficient release of von Willebrand factor."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": " VAMP3 is also central to cytokine secretion, being implicated in the regulated exocytosis of pro-inflammatory mediators from dendritic cells"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": ", keratinocytes"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": ", and fibroblast-like synoviocytes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "12"}]}, {"type": "t", "text": " Its role extends to immune synapse assembly and even ciliogenesis in T-cells"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "13"}]}, {"type": "t", "text": ", and it is exploited during pathogen entry: for instance, in Yersinia-containing vacuoles"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "14"}]}, {"type": "t", "text": "and via incorporation into herpesvirus glycoprotein complexes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "15"}]}, {"type": "t", "text": " Finally, under disturbed flow conditions, VAMP3 contributes to intercellular communication through the regulated secretion and transfer of microRNAs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "17"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its core trafficking functions, dysregulation of VAMP3 has important disease implications. Altered expression of VAMP3—modulated by non-coding RNA networks such as changes in ANRIL transcripts—is associated with an increased risk of coronary artery disease and periodontitis"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "18"}]}, {"type": "t", "text": ", and its misregulation in vascular smooth muscle cells via circular RNAs influences cellular proliferation and inflammatory responses in atherosclerosis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "19"}]}, {"type": "t", "text": " In the nervous system, VAMP3 contributes to the release of neuromodulators like D-serine, implicating it in the pathophysiology of bipolar affective disorder."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "20"}]}, {"type": "t", "text": " Moreover, a CEBPD/VAMP3 regulatory axis has been identified as a contributor to chemoresistance and immune evasion in triple-negative breast cancer."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "21"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Kevin Luftman, Nazarul Hasan, Paul Day, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Silencing of VAMP3 inhibits cell migration and integrin-mediated adhesion."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2009.01.036"}], "href": "https://doi.org/10.1016/j.bbrc.2009.01.036"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19159614"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19159614"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Claudio Marcelo Fader, Diego Germán Sánchez, María Belén Mestre, et al. "}, {"type": "b", "children": [{"type": "t", "text": "TI-VAMP/VAMP7 and VAMP3/cellubrevin: two v-SNARE proteins involved in specific steps of the autophagy/multivesicular body pathways."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochim Biophys Acta (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbamcr.2009.09.011"}], "href": "https://doi.org/10.1016/j.bbamcr.2009.09.011"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19781582"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19781582"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Michelle J Kean, Karla C Williams, Michael Skalski, et al. "}, {"type": "b", "children": [{"type": "t", "text": "VAMP3, syntaxin-13 and SNAP23 are involved in secretion of matrix metalloproteinases, degradation of the extracellular matrix and cell invasion."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.052761"}], "href": "https://doi.org/10.1242/jcs.052761"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19910495"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19910495"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Krista A Riggs, Nazarul Hasan, David Humphrey, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Regulation of integrin endocytic recycling and chemotactic cell migration by syntaxin 6 and VAMP3 interaction."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.102566"}], "href": "https://doi.org/10.1242/jcs.102566"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22573826"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22573826"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Yasuo Yamazaki, Christina Schönherr, Gaurav K Varshney, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Goliath family E3 ligases regulate the recycling endosome pathway via VAMP3 ubiquitylation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/emboj.2013.1"}], "href": "https://doi.org/10.1038/emboj.2013.1"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23353890"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23353890"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Marko Jović, Michelle J Kean, Anna Dubankova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Endosomal sorting of VAMP3 is regulated by PI4K2A."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.148809"}], "href": "https://doi.org/10.1242/jcs.148809"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25002402"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25002402"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Takashi Nozawa, Atsuko Minowa-Nozawa, Chihiro Aikawa, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The STX6-VTI1B-VAMP3 complex facilitates xenophagy by regulating the fusion between recycling endosomes and autophagosomes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Autophagy (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/15548627.2016.1241924"}], "href": "https://doi.org/10.1080/15548627.2016.1241924"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27791468"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27791468"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "János Polgár, Sul-Hee Chung, Guy L Reed "}, {"type": "b", "children": [{"type": "t", "text": "Vesicle-associated membrane protein 3 (VAMP-3) and VAMP-8 are present in human platelets and are required for granule secretion."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Blood (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1182/blood.v100.3.1081"}], "href": "https://doi.org/10.1182/blood.v100.3.1081"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12130530"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12130530"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Inés Rojo Pulido, Reinhard Jahn, Volker Gerke "}, {"type": "b", "children": [{"type": "t", "text": "VAMP3 is associated with endothelial weibel-palade bodies and participates in their Ca(2+)-dependent exocytosis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochim Biophys Acta (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbamcr.2010.11.007"}], "href": "https://doi.org/10.1016/j.bbamcr.2010.11.007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21094665"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21094665"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Daniëlle Rianne José Verboogen, Natalia González Mancha, Martin Ter Beest, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Genome-wide small interfering RNA screens reveal VAMP3 as a novel host factor required for Uukuniemi virus late penetration."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Virol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/JVI.00388-14"}], "href": "https://doi.org/10.1128/JVI.00388-14"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24850728"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24850728"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Laure-Anne Ligeon, Kevin Moreau, Nicolas Barois, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Association study between genetic variants at the VAMP2 and VAMP3 loci and bipolar affective disorder."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Psychiatr Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1097/YPG.0b013e3283050a83"}], "href": "https://doi.org/10.1097/YPG.0b013e3283050a83"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18628682"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18628682"}]}, {"type": "r", "ref": 21, "children": [{"type": "t", "text": "Yan Zhao, Yangyang Yu, Xiangmin Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCAAT enhancer binding protein delta activates vesicle associated membrane protein 3 transcription to enhance chemoresistance and extracellular PD-L1 expression in triple-negative breast cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Exp Clin Cancer Res (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s13046-024-03041-8"}], "href": "https://doi.org/10.1186/s13046-024-03041-8"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38627816"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38627816"}]}]}]}
Synonyms	CEB
Proteins	VAMP3_HUMAN
NCBI Gene ID	9341
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

VAMP3 has 7,603 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 126 datasets.

Click the + buttons to view associations for VAMP3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

VAMP3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of VAMP3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of VAMP3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of VAMP3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of VAMP3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of VAMP3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of VAMP3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of VAMP3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of VAMP3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of VAMP3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of VAMP3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of VAMP3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of VAMP3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with VAMP3 protein from the CCLE Cell Line Proteomics dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of VAMP3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of VAMP3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of VAMP3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of VAMP3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing VAMP3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing VAMP3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with VAMP3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with VAMP3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing VAMP3 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of VAMP3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with VAMP3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with VAMP3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with VAMP3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with VAMP3 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of VAMP3 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by VAMP3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with VAMP3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with VAMP3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with VAMP3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with VAMP3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with VAMP3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at VAMP3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of VAMP3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of VAMP3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing VAMP3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with VAMP3 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with VAMP3 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.