Browse VAMP3

Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Membrane Single-pass type IV membrane protein Cell junction, synapse, synaptosome
Domain PF00957 Synaptobrevin
Function

SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network.

> Gene Ontology
 
Biological Process GO:0001881 receptor recycling
GO:0001919 regulation of receptor recycling
GO:0001921 positive regulation of receptor recycling
GO:0006887 exocytosis
GO:0006904 vesicle docking involved in exocytosis
GO:0006906 vesicle fusion
GO:0007009 plasma membrane organization
GO:0007034 vacuolar transport
GO:0016050 vesicle organization
GO:0016197 endosomal transport
GO:0016482 cytosolic transport
GO:0017156 calcium ion regulated exocytosis
GO:0022406 membrane docking
GO:0031589 cell-substrate adhesion
GO:0034446 substrate adhesion-dependent cell spreading
GO:0035493 SNARE complex assembly
GO:0042147 retrograde transport, endosome to Golgi
GO:0043001 Golgi to plasma membrane protein transport
GO:0043112 receptor metabolic process
GO:0044801 single-organism membrane fusion
GO:0045055 regulated exocytosis
GO:0048278 vesicle docking
GO:0048284 organelle fusion
GO:0051048 negative regulation of secretion
GO:0051051 negative regulation of transport
GO:0061025 membrane fusion
GO:0072657 protein localization to membrane
GO:0072659 protein localization to plasma membrane
GO:0090002 establishment of protein localization to plasma membrane
GO:0090150 establishment of protein localization to membrane
GO:0090174 organelle membrane fusion
GO:1903531 negative regulation of secretion by cell
GO:1990778 protein localization to cell periphery
Molecular Function GO:0000149 SNARE binding
GO:0005484 SNAP receptor activity
GO:0017075 syntaxin-1 binding
GO:0019905 syntaxin binding
Cellular Component GO:0005802 trans-Golgi network
GO:0016324 apical plasma membrane
GO:0030133 transport vesicle
GO:0030135 coated vesicle
GO:0030136 clathrin-coated vesicle
GO:0030141 secretory granule
GO:0030659 cytoplasmic vesicle membrane
GO:0030662 coated vesicle membrane
GO:0030665 clathrin-coated vesicle membrane
GO:0031201 SNARE complex
GO:0031984 organelle subcompartment
GO:0032588 trans-Golgi network membrane
GO:0045177 apical part of cell
GO:0055037 recycling endosome
GO:0098791 Golgi subcompartment
GO:0099503 secretory vesicle
> KEGG and Reactome Pathway
 
KEGG hsa04130 SNARE interactions in vesicular transport
hsa04145 Phagosome
Reactome R-HSA-1280218: Adaptive Immune System
R-HSA-1236975: Antigen processing-Cross presentation
R-HSA-8856825: Cargo recognition for clathrin-mediated endocytosis
R-HSA-983169: Class I MHC mediated antigen processing & presentation
R-HSA-8856828: Clathrin-mediated endocytosis
R-HSA-1236974: ER-Phagosome pathway
R-HSA-168256: Immune System
R-HSA-6811442: Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991: Membrane Trafficking
R-HSA-6811440: Retrograde transport at the Trans-Golgi-Network
R-HSA-5653656: Vesicle-mediated transport
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between VAMP3 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 
  Literatures describing the relation between VAMP3 and anti-tumor immunity in human cancer.
PMID Cancer type Relation to immunity Evidence sentences
29363545Lung carcinomaPromote immunityTumor conditioned DC exhibited downregulation of the SNARE VAMP3, a regulator of endosomes trafficking we found to be required for cross-presentation of tumor antigens and DC-mediated tumor rejection.
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of VAMP3 in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of VAMP3 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.080.733
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.1450.961
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.2330.906
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.1090.645
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.1070.946
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.1110.954
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.140.75
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.0020.999
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-0.3330.881
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.5650.761
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 281.0220.72
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.040.5
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of VAMP3 in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 141705.9-5.91
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 41407.1-7.11
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27730001
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27590001
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of VAMP3. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of VAMP3. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by VAMP3.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of VAMP3. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of VAMP3 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between VAMP3 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolVAMP3
Namevesicle-associated membrane protein 3
Aliases CEB; cellubrevin; VAMP-3; synaptobrevin-3
Chromosomal Location1p36.23
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting VAMP3 collected from DrugBank database.
> Drugs from DrugBank database
 

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