VAMP2

vesicle associated membrane protein 2 | VAMP-2, SYB2

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]

Member of: DE-1 DE-1.2

Biological processes 73 terms

Golgi to plasma membrane protein transport (GO:0043001)SNAP receptor activity (GO:0005484)SNARE binding (GO:0000149)SNARE complex (GO:0031201)SNARE complex (GO:0031201)SNARE complex (GO:0031201)SNARE complex assembly (GO:0035493)calcium-dependent protein binding (GO:0048306)calcium-ion regulated exocytosis (GO:0017156)calmodulin binding (GO:0005516)cellular response to insulin stimulus (GO:0032869)clathrin-coated endocytic vesicle membrane (GO:0030669)clathrin-coated vesicle (GO:0030136)clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)cytoplasmic vesicle (GO:0031410)cytosol (GO:0005829)eosinophil degranulation (GO:0043308)exocytosis (GO:0006887)long-term synaptic potentiation (GO:0060291)membrane (GO:0016020)membrane (GO:0016020)membrane fusion (GO:0061025)mucus secretion (GO:0070254)natural killer cell degranulation (GO:0043320)neuron projection (GO:0043005)neuron projection terminus (GO:0044306)neurotransmitter secretion (GO:0007269)neutrophil degranulation (GO:0043312)perinuclear region of cytoplasm (GO:0048471)phospholipid binding (GO:0005543)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of intracellular protein transport (GO:0090316)presynaptic membrane (GO:0042734)protein binding (GO:0005515)protein transport (GO:0015031)protein-containing complex assembly (GO:0065003)regulation of delayed rectifier potassium channel activity (GO:1902259)regulation of exocytosis (GO:0017157)regulation of histamine secretion by mast cell (GO:1903593)regulation of vesicle-mediated transport (GO:0060627)response to glucose (GO:0009749)secretory granule (GO:0030141)secretory granule membrane (GO:0030667)secretory granule membrane (GO:0030667)synapse (GO:0045202)synaptic vesicle (GO:0008021)synaptic vesicle (GO:0008021)synaptic vesicle endocytosis (GO:0048488)synaptic vesicle exocytosis (GO:0016079)synaptic vesicle exocytosis (GO:0016079)synaptic vesicle membrane (GO:0030672)synaptic vesicle membrane (GO:0030672)synaptic vesicle membrane (GO:0030672)synaptic vesicle membrane (GO:0030672)synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)syntaxin binding (GO:0019905)trans-Golgi network (GO:0005802)transport vesicle (GO:0030133)vesicle (GO:0031982)vesicle fusion (GO:0006906)vesicle fusion (GO:0006906)vesicle fusion (GO:0006906)vesicle-mediated transport (GO:0016192)vesicle-mediated transport (GO:0016192)voltage-gated potassium channel complex (GO:0008076)zymogen granule membrane (GO:0042589)

Expression (TPM)

TFs regulating VAMP2 0 TFs

Transcription factors with Perturb-seq knockdown data for VAMP2. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = VAMP2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to VAMP2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of VAMP2, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr17:7,885,205–7,885,734	277.6 kb	Distal (>10kb) Multiome	371
chr17:7,887,616–7,888,198	275.1 kb	Distal (>10kb) Multiome	581
chr17:7,915,430–7,916,499	247.0 kb	Distal (>10kb) Multiome	869
chr17:7,922,863–7,923,421	239.9 kb	Distal (>10kb) Multiome	205
chr17:7,929,559–7,930,172	233.1 kb	Distal (>10kb) Multiome	106
chr17:7,931,533–7,932,876	230.9 kb	Distal (>10kb) Multiome	767
chr17:7,971,685–7,972,375	191.0 kb	Distal (>10kb) Multiome	45
chr17:7,989,908–7,990,676	172.6 kb	Distal (>10kb) Multiome	652
chr17:8,015,966–8,016,968	146.9 kb	Distal (>10kb) Multiome	339
chr17:8,068,609–8,069,844	94.1 kb	Distal (>10kb) Multiome	100
chr17:8,079,261–8,080,640	83.5 kb	Distal (>10kb) Multiome	613
chr17:8,109,567–8,110,530	52.7 kb	Distal (>10kb) Multiome	360
chr17:8,117,780–8,119,396	44.0 kb	Distal (>10kb) Multiome	684
chr17:8,119,590–8,122,560	42.3 kb	Distal (>10kb) Multiome	968
chr17:8,123,407–8,124,386	38.8 kb	Distal (>10kb) Multiome	296
chr17:8,125,308–8,126,995	37.2 kb	Distal (>10kb) Multiome	724
chr17:8,138,425–8,139,804	24.0 kb	Distal (>10kb) Multiome	981
chr17:8,151,026–8,151,640	11.7 kb	Distal (>10kb) Multiome	435
chr17:8,151,914–8,152,786	10.4 kb	Distal (>10kb) Multiome	633
chr17:8,153,878–8,154,864	8.6 kb	Proximal (<10kb) Multiome	644
chr17:8,155,928–8,157,418	6.3 kb	Proximal (<10kb) Multiome	789
chr17:8,158,672–8,159,039	3.9 kb	Proximal (<10kb)	350
chr17:8,162,377–8,163,907	106 bp	At TSS Multiome	637
chr17:8,164,190–8,164,640	1.2 kb	Proximal (<10kb)	503
chr17:8,172,460–8,174,346	10.6 kb	Distal (>10kb) Multiome	1196
chr17:8,175,900–8,176,943	13.5 kb	Distal (>10kb) Multiome	601
chr17:8,185,937–8,188,084	24.8 kb	Distal (>10kb) Multiome	1065
chr17:8,189,376–8,190,688	27.3 kb	Distal (>10kb) Multiome	748
chr17:8,192,025–8,192,719	29.4 kb	Distal (>10kb) Multiome	452
chr17:8,210,139–8,210,786	47.7 kb	Distal (>10kb) Multiome	778
chr17:8,220,662–8,224,088	60.0 kb	Distal (>10kb) Multiome	1171
chr17:8,226,529–8,227,280	63.8 kb	Distal (>10kb) Multiome	565
chr17:8,247,519–8,249,589	86.4 kb	Distal (>10kb) Multiome	914
chr17:8,288,100–8,289,230	125.9 kb	Distal (>10kb) Multiome	751
chr17:8,295,073–8,296,021	132.6 kb	Distal (>10kb) Multiome	739
chr17:8,310,033–8,310,555	147.3 kb	Distal (>10kb) Multiome	98
chr17:8,313,329–8,313,824	150.6 kb	Distal (>10kb) Multiome	30
chr17:8,376,215–8,376,918	213.7 kb	Distal (>10kb) Multiome	888
chr17:8,382,925–8,384,028	220.5 kb	Distal (>10kb) Multiome	981
chr17:8,435,307–8,436,885	272.9 kb	Distal (>10kb) Multiome	847

Genome Browser

Genomic view of the VAMP2 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.