VAMP7 vesicle associated membrane protein 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VAMP7provided by HGNC
Official Full Name: vesicle associated membrane protein 7provided by HGNC
Primary source: HGNC:HGNC:11486
See related: Ensembl:ENSG00000124333 MIM:300053
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SYBL1; TIVAMP; VAMP-7; TI-VAMP
Summary: This gene encodes a transmembrane protein that is a member of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) family. The encoded protein localizes to late endosomes and lysosomes and is involved in the fusion of transport vesicles to their target membranes. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]
Expression: Ubiquitous expression in placenta (RPKM 18.0), kidney (RPKM 17.3) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: Xq28 and Yq12

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	X	NC_000023.11 (155881318..155943769)
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	Y	NC_000024.10 (57067838..57130289)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (155110943..155173433)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (59213949..59276439)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Chromosome Y - NC_000024.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The pseudoautosomal region of human X and Y chromosome encoded VAMP7 protein was predicted to interact with at least 22 proteins encoded on the somatic chromosomes.
Title: Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions.
GLUT5 required an interaction cascade of Rab11, Myo5B, Slp4a, Munc18-2, and Vamp7 with Stx3.
Title: Cargo-selective apical exocytosis in epithelial cells is conducted by Myo5B, Slp4a, Vamp7, and Syntaxin 3.
VAMP-7 participates in both platelet granule secretion and spreading and suggest a mechanism whereby VAMP-7 links granule exocytosis with actin reorganization.
Title: VAMP-7 links granule exocytosis to actin reorganization during platelet activation.
highlight the role that VAMP3 and VAMP7 play in selection of the pathways leading to generation of ultrastructurally different LC3 compartments
Title: Role of VAMP3 and VAMP7 in the commitment of Yersinia pseudotuberculosis to LC3-associated pathways involving single- or double-membrane vacuoles.
Increased level of SNAP23-Syntaxin4-VAMP7 interaction correlates with decreased Syntaxin4 phosphorylation and trafficking of MT1-MMP to invadopodia during cellular invasion.
Title: SNAP23, Syntaxin4, and vesicle-associated membrane protein 7 (VAMP7) mediate trafficking of membrane type 1-matrix metalloproteinase (MT1-MMP) during invadopodium formation and tumor cell invasion.
increased gene dosage of VAMP7, and thus higher expression levels of its protein product, enhances estrogen receptor action in male genitourinary tissues
Title: Increased gene copy number of VAMP7 disrupts human male urogenital development through altered estrogen action.
CALM is able to sort VAMP4 and VAMP7, even though they have sorting signals for other clathrin adaptors.
Title: Uncoupling the functions of CALM in VAMP sorting and clathrin-coated pit formation.
Overexpression of Vamp7 inhibited the heterotypic fusion with lysosomes and the homotypic fusion between individual Coxiella phagosomes and replicative vacuoles.
Title: Endocytic SNAREs are involved in optimal Coxiella burnetii vacuole development.
Activation of TI-VAMP-mediated exocytosis thus relies on tyrosine phosphorylation.
Title: Increased activity of the vesicular soluble N-ethylmaleimide-sensitive factor attachment protein receptor TI-VAMP/VAMP7 by tyrosine phosphorylation in the Longin domain.
hVps41 and VAMP7 are specifically involved in the fusion of trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes.
Title: hVps41 and VAMP7 function in direct TGN to late endosome transport of lysosomal membrane proteins.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated (2012-09-06) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated (2012-09-06) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Inhibition of endocytosis by siRNA-mediated depletion of EPS15, STX7, RAB7, and VAMP7 restores Gag/p24 expression in the presence of APOL1	PubMed
	gag	HIV-1 Gag accumulates in late endosome and co-localizes with TiVamp as a result of disruption of endosomal pathways	PubMed
	gag	HIV-1 Gag and genomic RNA are transported on endosomal vesicles, in which endosomal protein TiVamp is co-localized and involved in fusion events with the plasma membrane	PubMed
capsid	gag	Inhibition of endocytosis by siRNA-mediated depletion of EPS15, STX7, RAB7, and VAMP7 restores Gag/p24 expression in the presence of APOL1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:154379

SYBL1 (e-PCR)
- UniSTS:506668

GDB:451553 (e-PCR)
- UniSTS:99753

RH70940 (e-PCR)
- UniSTS:88813

Homology

Homologs of the VAMP7 gene: The VAMP7 gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 318 organisms have orthologs with human gene VAMP7
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
SNARE binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
syntaxin binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
ER to Golgi vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
Golgi to plasma membrane protein transport	IEA Inferred from Electronic Annotation more info
SNARE complex assembly	IEA Inferred from Electronic Annotation more info
NOT autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
calcium ion regulated exocytosis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
endosome to lysosome transport	IDA Inferred from Direct Assay more info	PubMed
eosinophil degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
eosinophil degranulation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
exocytosis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
membrane organization	TAS Traceable Author Statement more info
natural killer cell degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
neutrophil degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
neutrophil degranulation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
phagocytosis, engulfment	ISS Inferred from Sequence or Structural Similarity more info	PubMed
positive regulation of dendrite morphogenesis	IEA Inferred from Electronic Annotation more info
positive regulation of histamine secretion by mast cell	IMP Inferred from Mutant Phenotype more info	PubMed
post-Golgi vesicle-mediated transport	TAS Traceable Author Statement more info
regulation of protein targeting to vacuolar membrane	IEA Inferred from Electronic Annotation more info
triglyceride transport	IEA Inferred from Electronic Annotation more info
vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info	PubMed
vesicle fusion	IDA Inferred from Direct Assay more info	PubMed
vesicle fusion with Golgi apparatus	IEA Inferred from Electronic Annotation more info
vesicle transport along microtubule	IEA Inferred from Electronic Annotation more info
vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
SNARE complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
SNARE complex	IDA Inferred from Direct Assay more info	PubMed
SNARE complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
apical part of cell	IEA Inferred from Electronic Annotation more info
azurophil granule membrane	IDA Inferred from Direct Assay more info	PubMed
cell	IEA Inferred from Electronic Annotation more info
cell surface	IEA Inferred from Electronic Annotation more info
clathrin-coated vesicle membrane	TAS Traceable Author Statement more info
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
extracellular exosome	HDA more info	PubMed
filopodium	IEA Inferred from Electronic Annotation more info
hippocampal mossy fiber to CA3 synapse	IEA Inferred from Electronic Annotation more info
integral component of synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
lamellipodium	IDA Inferred from Direct Assay more info	PubMed
late endosome membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
lysosomal membrane	HDA more info	PubMed
lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
lysosomal membrane	TAS Traceable Author Statement more info
membrane	IDA Inferred from Direct Assay more info	PubMed
neuron projection	ISS Inferred from Sequence or Structural Similarity more info
perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
phagocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info	PubMed
phagocytic vesicle membrane	IEA Inferred from Electronic Annotation more info
plasma membrane	IDA Inferred from Direct Assay more info	PubMed
plasma membrane	TAS Traceable Author Statement more info
platelet alpha granule	IDA Inferred from Direct Assay more info	PubMed
pseudopodium	IDA Inferred from Direct Assay more info	PubMed
secretory granule	IDA Inferred from Direct Assay more info	PubMed
secretory granule membrane	IDA Inferred from Direct Assay more info	PubMed
trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vesicle-associated membrane protein 7

Names: synaptobrevin-like 1; synaptobrevin-like protein 1; tetanus neurotoxin-insensitive VAMP; tetanus-insensitive VAMP

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_021435.1 RefSeqGene

Range

5066..67491

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145149.3 → NP_001138621.1 vesicle-associated membrane protein 7 isoform 2

See identical proteins and their annotated locations for NP_001138621.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AI522002, AJ271736, AJ549301, X92396

Consensus CDS

CCDS48199.1

UniProtKB/Swiss-Prot

P51809

Related

ENSP00000427822.1, ENST00000460621.6

Conserved Domains (2) summary

cd15871
Location:83 → 147

R-SNARE_VAMP7; SNARE motif of VAMP7

cl26083
Location:31 → 131

Synaptobrevin; Synaptobrevin
NM_001185183.2 → NP_001172112.1 vesicle-associated membrane protein 7 isoform 3

See identical proteins and their annotated locations for NP_001172112.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is longer and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AI522002, AJ271736, AJ295938

Consensus CDS

CCDS55548.1

UniProtKB/Swiss-Prot

P51809

UniProtKB/TrEMBL

A0A024R074

Related

ENSP00000262640.6, ENST00000262640.11

Conserved Domains (2) summary

pfam13774
Location:29 → 104

Longin; Regulated-SNARE-like domain

cl22856
Location:124 → 144

SNARE; SNARE motif
NM_005638.6 → NP_005629.1 vesicle-associated membrane protein 7 isoform 1

See identical proteins and their annotated locations for NP_005629.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1).

Source sequence(s)

AI522002, BC056141

Consensus CDS

CCDS14770.4

UniProtKB/Swiss-Prot

P51809

UniProtKB/TrEMBL

A0A024R061

Related

ENSP00000286448.6, ENST00000286448.12

Conserved Domains (2) summary

cd15871
Location:124 → 188

R-SNARE_VAMP7; SNARE motif of VAMP7

cd14824
Location:4 → 116

Longin; longin domain

RNA

NR_033714.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI522002, AJ271736, AK297385, X92396
NR_033715.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI522002, AJ271736, AK295605, X92396

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p13 Primary Assembly

Range

155881318..155943769

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017029760.1 → XP_016885249.1 vesicle-associated membrane protein 7 isoform X2

Conserved Domains (2) summary

cd15871
Location:77 → 141

R-SNARE_VAMP7; SNARE motif of VAMP7

cd14824
Location:3 → 69

Longin; longin domain
XM_011531188.1 → XP_011529490.1 vesicle-associated membrane protein 7 isoform X1

See identical proteins and their annotated locations for XP_011529490.1

Conserved Domains (2) summary

pfam13774
Location:3 → 51

Longin; Regulated-SNARE-like domain

cl22856
Location:77 → 97

SNARE; SNARE motif

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000024.10 Reference GRCh38.p13 Primary Assembly

Range

57067838..57130289

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017030063.1 → XP_016885552.1 vesicle-associated membrane protein 7 isoform X2

Conserved Domains (2) summary

cd15871
Location:77 → 141

R-SNARE_VAMP7; SNARE motif of VAMP7

cd14824
Location:3 → 69

Longin; longin domain
XM_011545653.1 → XP_011543955.1 vesicle-associated membrane protein 7 isoform X1

See identical proteins and their annotated locations for XP_011543955.1

Conserved Domains (2) summary

pfam13774
Location:3 → 51

Longin; Regulated-SNARE-like domain

cl22856
Location:77 → 97

SNARE; SNARE motif