AiPD: Autoinhibited Protein Database

O75379

Gene name	VAMP4
Protein name	Vesicle-associated membrane protein 4
Names	VAMP-4
Species	Homo sapiens (Human)
KEGG Pathway	hsa:8674
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

1-127 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

1-127 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

1 structures for O75379

Entry ID	Method	Resolution	Chain	Position	Source
AF-O75379-F1	Predicted				AlphaFoldDB

105 variants for O75379

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
rs781610287 CA1244498	2	P>L		No	ClinGen ExAC gnomAD
CA343720845 rs1234972291	6	K>*		No	ClinGen gnomAD
CA343720844 rs1183080083	6	K>T		No	ClinGen gnomAD
CA1244497 rs535997142	7	R>C	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
CA343720838 rs535997142	7	R>G		No	ClinGen ExAC TOPMed gnomAD
rs751766048 CA1244496	7	R>H	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
rs766286990 CA1244495	10	N>S		No	ClinGen ExAC gnomAD
CA343720802 rs1476049478	12	D>G		No	ClinGen TOPMed
rs1476049478 CA343720801	12	D>V		No	ClinGen TOPMed
CA1244493 rs567836066	14	V>A		No	ClinGen 1000Genomes ExAC
rs145814595 CA1244492	15	T>S		No	ClinGen ESP ExAC TOPMed gnomAD
TCGA novel	17	S>Y	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs201528503 CA1244490	22	R>K		No	ClinGen ESP ExAC TOPMed gnomAD
rs201528503 CA1244489	22	R>T		No	ClinGen ESP ExAC TOPMed gnomAD
COSM278067 rs1242626137 CA343717684	23	R>I	Variant assessed as Somatic; 0.0 impact. large_intestine endometrium [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA TOPMed gnomAD
CA343717678 rs1201934317	24	N>S		No	ClinGen gnomAD
CA1244479 rs781416958	28	D>G		No	ClinGen ExAC TOPMed gnomAD
CA1244478 rs771383257	29	D>H		No	ClinGen ExAC TOPMed gnomAD
CA32671428 rs771383257	29	D>Y		No	ClinGen ExAC TOPMed gnomAD
CA32671420 rs199778923	31	D>E		No	ClinGen 1000Genomes
CA343717629 rs1417131393	31	D>G		No	ClinGen TOPMed
rs1205542475 CA343717617	33	E>K		No	ClinGen gnomAD
CA1244477 rs747257774	35	D>H		No	ClinGen ExAC gnomAD
rs778190208 CA1244476	36	F>I		No	ClinGen ExAC gnomAD
rs771441555 CA32665911	40	G>V		No	ClinGen TOPMed
CA32665907 rs955936667	41	P>L		No	ClinGen Ensembl
rs1558109516 CA343717058	41	P>S		No	ClinGen Ensembl
rs141906655 CA1244461	42	S>P		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA343717015 rs1469548304	44	P>S		No	ClinGen TOPMed
CA1244460 rs759993177	48	P>T		No	ClinGen ExAC TOPMed gnomAD
CA343716965 rs1365548408	49	R>K		No	ClinGen gnomAD
TCGA novel	50	N>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs777230369 CA1244459	52	K>N		No	ClinGen ExAC TOPMed gnomAD
CA1244458 rs145867825	54	K>R		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs761249966 CA1244435	55	H>Q		No	ClinGen ExAC gnomAD
rs1163600004 CA343715897	59	Q>R		No	ClinGen TOPMed
CA343715834 rs1364905725	62	E>A		No	ClinGen TOPMed
rs748346948 CA1244432	64	I>T		No	ClinGen ExAC gnomAD
rs1297653243 CA343715753	66	V>D		No	ClinGen gnomAD
rs774580642 CA1244431	67	M>I		No	ClinGen ExAC gnomAD
CA32661473 rs951628126	67	M>V		No	ClinGen TOPMed
CA32661471 rs1052670	68	Q>P		No	ClinGen Ensembl
CA1244430 rs768735104	70	N>S		No	ClinGen ExAC gnomAD
TCGA novel	71	I>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA343715628 rs1337571964	73	K>E		No	ClinGen gnomAD
CA32661435 rs200788972	78	G>R		No	ClinGen TOPMed
TCGA novel	78	G>W	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1277997742 CA343715438	82	D>G		No	ClinGen TOPMed
rs1469491171 CA343715448	82	D>N		No	ClinGen gnomAD
CA1244429 rs183763963	83	E>A		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA343715341 rs368840676	87	K>*		No	ClinGen ESP TOPMed
rs368840676 CA32661395	87	K>E		No	ClinGen ESP TOPMed
rs368840676 CA32661400	87	K>Q		No	ClinGen ESP TOPMed
rs756061887 CA1244427	87	K>T		No	ClinGen ExAC TOPMed gnomAD
rs919432061 CA32661385	88	S>*		No	ClinGen Ensembl
rs935768514 CA32660655	91	L>F		No	ClinGen TOPMed gnomAD
CA32660665 rs986278032	91	L>V		No	ClinGen Ensembl
CA343715110 rs1333063136	92	S>L		No	ClinGen gnomAD
CA1244408 rs745830452	92	S>P		No	ClinGen ExAC TOPMed gnomAD
rs745830452 CA1244407	92	S>T		No	ClinGen ExAC TOPMed gnomAD
rs112184910 CA32660605	94	N>D		No	ClinGen Ensembl
CA32660588 rs902902950	96	T>I		No	ClinGen TOPMed
rs746888610 CA343715029	97	A>G		No	ClinGen ExAC gnomAD
CA1244404 rs746888610	97	A>V		No	ClinGen ExAC gnomAD
CA1244403 rs777416517	99	S>N		No	ClinGen ExAC gnomAD
CA1244402 rs758136623	101	R>G		No	ClinGen ExAC gnomAD
TCGA novel	101	R>S	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA1244401 rs752329350	102	S>A		No	ClinGen ExAC gnomAD
rs1021254914 CA32660528	102	S>Y		No	ClinGen TOPMed
CA32660522 rs758825644	103	K>I		No	ClinGen Ensembl
TCGA novel	105	L>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
COSM172094 CA32660493 rs577477919	106	R>*	Variant assessed as Somatic; 0.0 impact. large_intestine [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA gnomAD
CA1244399 rs754485864	106	R>Q		No	ClinGen ExAC TOPMed gnomAD
rs1572239668 CA343714830	108	Q>*		No	ClinGen Ensembl
CA1244398 rs149851036	108	Q>R		No	ClinGen ESP ExAC TOPMed gnomAD
CA1244395 rs751971096	109	M>I		No	ClinGen ExAC TOPMed gnomAD
CA1244396 rs762218411	109	M>V		No	ClinGen ExAC gnomAD
CA1244394 rs764302072	110	W>C		No	ClinGen ExAC gnomAD
rs375741911 CA32660451	112	R>C	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen ESP NCI-TCGA
CA1244393 rs373661099	112	R>H		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA343714714 rs1490975865	113	G>A		No	ClinGen gnomAD
CA32660436 rs899770691	114	C>Y		No	ClinGen TOPMed
CA1244392 rs775643184	115	K>R		No	ClinGen ExAC TOPMed gnomAD
CA1244382 rs778754518	117	K>N		No	ClinGen ExAC gnomAD
CA1244381 rs377614084	118	A>T		No	ClinGen ESP ExAC TOPMed gnomAD
rs753450848 CA1244380	118	A>V		No	ClinGen ExAC gnomAD
CA343712973 rs1488893398	120	M>I		No	ClinGen Ensembl
CA1244379 rs779377304	120	M>V		No	ClinGen ExAC gnomAD
rs757791904 CA1244378	123	V>D		No	ClinGen ExAC gnomAD
rs751972487 CA1244377	124	A>S		No	ClinGen ExAC gnomAD
rs764468160 CA1244376	125	A>V		No	ClinGen ExAC gnomAD
rs1457479692 CA343712942	126	I>V		No	ClinGen gnomAD
CA343712934 rs1405945697	127	L>F		No	ClinGen gnomAD
CA1244373 rs765510273	130	V>G		No	ClinGen ExAC
rs759741968 CA1244372	133	I>F		No	ClinGen ExAC TOPMed gnomAD
rs759741968 CA343712898	133	I>V		No	ClinGen ExAC TOPMed gnomAD
CA32656746 rs147472171	134	L>H		No	ClinGen ESP
CA1244362 rs768476809	134	L>V		No	ClinGen ExAC gnomAD
rs748829095 CA1244361	135	I>T		No	ClinGen ExAC TOPMed gnomAD
rs779649774 CA1244360	136	V>A		No	ClinGen ExAC gnomAD
rs755533471 CA1244359	137	M>V		No	ClinGen ExAC gnomAD
rs1383124387 CA343712784	140	R>C		No	ClinGen gnomAD
CA1244358 rs745362209	140	R>H		No	ClinGen ExAC TOPMed gnomAD
CA343712768 rs1572236317	141	T>I		No	ClinGen Ensembl
CA343712760 rs1413177349	142	T>L		No	ClinGen gnomAD

No associated diseases with O75379

1 regional properties for O75379

Type	Name	Position	InterPro Accession
conserved_site	Peptidyl-tRNA hydrolase, conserved site	107 - 117	IPR018171

Functions

		Description
EC Number
Subcellular Localization	Golgi apparatus, trans-Golgi network membrane ; Single-pass type IV membrane protein	Associated with trans Golgi network (TGN) and newly formed immature secretory granules (ISG) Not found on the mature secretory organelles
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

13 GO annotations of cellular component

Name	Definition
cell surface	The external part of the cell wall and/or plasma membrane.
clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
endosome	A vacuole to which materials ingested by endocytosis are delivered.
Golgi apparatus	A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
lysosome	A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
SNARE complex	A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
trans-Golgi network	The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
trans-Golgi network membrane	The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

No GO annotations of molecular function

Name	Definition
No GO annotations for molecular function

6 GO annotations of biological process

Name	Definition
endocytic recycling	The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins.
Golgi ribbon formation	The formation of a continuous ribbon of interconnected Golgi stacks of flat cisternae.
microtubule cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
regulation of synaptic vesicle endocytosis	Any process that modulates the frequency, rate or extent of synaptic vesicle endocytosis.
SNARE complex assembly	The aggregation, arrangement and bonding together of a set of components to form a SNARE complex, a protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers.
synaptic vesicle to endosome fusion	Fusion of a synaptic vesicle with an endosome.

3 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
Q2KHY2	VAMP5	Vesicle-associated membrane protein 5	Bos taurus (Bovine)	PR
O70404	Vamp8	Vesicle-associated membrane protein 8	Mus musculus (Mouse)	PR
O70480	Vamp4	Vesicle-associated membrane protein 4	Mus musculus (Mouse)	PR

10	20	30	40	50	60
MPPKFKRHLN	DDDVTGSVKS	ERRNLLEDDS	DEEEDFFLRG	PSGPRFGPRN	DKIKHVQNQV
70	80	90	100	110	120
DEVIDVMQEN	ITKVIERGER	LDELQDKSES	LSDNATAFSN	RSKQLRRQMW	WRGCKIKAIM
130	140
ALVAAILLLV	IIILIVMKYR	T