Tbio VAMP2 Vesicle-associated membrane protein 2

Protein Summary

Description

Involved in the targeting and/or fusion of transport vesicles to their target membrane. Modulates the gating characteristics of the delayed rectifier voltage-dependent potassium channel KCNB1. The protein encoded by this gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. 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. This gene is thought to participate in neurotransmitter release at a step between docking and fusion. The protein forms a stable complex with syntaxin, synaptosomal-associated protein, 25 kD, and synaptotagmin. It also forms a distinct complex with synaptophysin. It is a likely candidate gene for familial infantile myasthenia (FIMG) because of its map location and because it encodes a synaptic vesicle protein of the type that has been implicated in the pathogenesis of FIMG. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• P63027
• P19065
• Q9BUC2
• VAMP-2

Gene Name

• VAMP2

Ensembl ID

• ENST00000316509
• ENSP00000314214
• ENSG00000220205

Symbol

• SYB2
• SYB2
• VAMP-2

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological process	0.99
disease perturbation	0.95
protein complex	0.94
cellular component	0.89
histone modification site profile	0.65

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Target Illumination GWAS Analytics (TIGA)

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GENEVA

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 540.66   (req: < 5)

Gene RIFs: 32   (req: <= 3)

Antibodies: 265   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 540.66   (req: >= 5)

Gene RIFs: 32   (req: > 3)

Antibodies: 265   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 25

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (2)

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
chronotype measurement	EFO_0008328	1	1	0	1.1	68.7
potassium measurement	EFO_0009283	1	1	1		4.1

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
chronotype measurement	EFO_0008328	0	1.1	68.7
potassium measurement	EFO_0009283	1		4.1

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Orthologs (1)

1 – 1 of 1

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	vesicle associated membrane protein 2		574134

Species	Name	OMA	EggNOG	Inparanoid
Macaque	vesicle associated membrane protein 2

Protein Data Bank (5)

1 – 5 of 5

PDB Structure Id	Ligand	Method	Resolution (Å)	M.W. (kDa)	Pub Year	Title

PDB Structure Id	M.W.	Resolution	Pub Year

Pathways (68)

Reactome (38)

KEGG (5)

PathwayCommons (22)

WikiPathways (3)

Acetylcholine Neurotransmitter Release Cycle (R-HSA-264642)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Acetylcholine Neurotransmitter Release Cycle	17 targets	R-HSA-264642
Reactome	Cargo recognition for clathrin-mediated endocytosis	105 targets	R-HSA-8856825
Reactome	Clathrin-mediated endocytosis	143 targets	R-HSA-8856828
Reactome	Cytokine Signaling in Immune system	922 targets	R-HSA-1280215
Reactome	Disease	1105 targets	R-HSA-1643685

Name	Explore in Pharos	Explore in Source
Acetylcholine Neurotransmitter Release Cycle	17 targets	R-HSA-264642
Cargo recognition for clathrin-mediated endocytosis	105 targets	R-HSA-8856825
Clathrin-mediated endocytosis	143 targets	R-HSA-8856828
Cytokine Signaling in Immune system	922 targets	R-HSA-1280215
Disease	1105 targets	R-HSA-1643685

Gene Ontology Terms (52)

Functions (7)

Components (27)

Processes (18)

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Items per page:

10

1 – 7 of 7

GO Term	Evidence	Assigned by
syntaxin binding	Inferred from Physical Interaction (IPI)	UniProtKB
calcium-dependent protein binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
calmodulin binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
phospholipid binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
SNARE binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
syntaxin-1 binding	Inferred from Sequence or structural Similarity (ISS)	ParkinsonsUK-UCL
protein self-association	Traceable Author Statement (TAS)	ParkinsonsUK-UCL

Protein-Protein Interactions (383)

Explore Interacting Targets

1 – 10 of 383

• See Interactions on String-DB

SYPL1

Tbio

Novelty: 0.04187055

p_int: 0.999758124

p_ni: 0.000241876

Score: 0.54

Data Source: BioPlex,STRINGDB

WDFY1

Tbio

Novelty: 0.13382544

p_int: 0.995197026

p_ni: 0.004802974

Score: 0.18

Data Source: BioPlex,STRINGDB

STX7

Tbio

Novelty: 0.03109969

p_int: 0.986151277

p_ni: 0.013848723

Score: 0.939

Data Source: BioPlex,STRINGDB

STX12

Tbio

Novelty: 0.03836262

p_int: 0.985251227

p_ni: 0.014748773

Score: 0.97

Data Source: BioPlex,STRINGDB

WASHC1

Tbio

Novelty: 0.09242196

p_int: 0.976419239

p_ni: 0.02358076

p_wrong: 1e-9

Data Source: BioPlex

STX19

Tdark

Novelty: 0.99387951

p_int: 0.941572852

p_ni: 0.058427148

Score: 0.792

Data Source: BioPlex,STRINGDB

TPCN2

Tchem

Family: IC

Novelty: 0.01351129

p_int: 0.884106036

p_ni: 0.115893927

p_wrong: 3.6e-8

Score: 0.156

Data Source: BioPlex,STRINGDB

STX11

Tbio

Novelty: 0.01670743

p_int: 0.881555206

p_ni: 0.118444794

Score: 0.889

Data Source: BioPlex,STRINGDB

MUC1

Tbio

Novelty: 0.00024203

p_int: 0.835239826

p_ni: 0.164759795

p_wrong: 3.79e-7

Score: 0.161

Data Source: BioPlex,STRINGDB

STX3

Tbio

Novelty: 0.01055819

p_int: 0.816612041

p_ni: 0.183387571

p_wrong: 3.87e-7

Score: 0.999

Data Source: BioPlex,STRINGDB

Publication Statistics

PubMed Score  540.66

PubMed score by year

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PubTator Score  265.27

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

3D-structure
Acetylation
Cell junction
Cell membrane
Coiled coil
Complete proteome
Cytoplasmic vesicle
Membrane
Phosphoprotein
Reference proteome

GWAS Trait Find Similar Targets

chronotype measurement
potassium measurement

MGI Phenotype Find Similar Targets

behavior/neurological phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
mortality/aging
nervous system phenotype