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
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Genomic context

Location:: Xq28 and Yq12

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
109.20211119	current	GRCh38.p13 (GCF_000001405.39)	X	NC_000023.11 (155881318..155943769)
109.20211119	current	GRCh38.p13 (GCF_000001405.39)	Y	NC_000024.10 (57067838..57130289)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (155111008..155173433)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (59214014..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?

A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers.
Title: A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers.
Organelle tethering, pore formation and SNARE compensation in the late endocytic pathway.
Title: Organelle tethering, pore formation and SNARE compensation in the late endocytic pathway.
A case series of infants with increased VAMP7 gene dosage at birth and virilization defects.
Title: A case series of infants with increased VAMP7 gene dosage at birth and virilization defects.
DIPK2A promotes STX17- and VAMP7-mediated autophagosome-lysosome fusion by binding to VAMP7B.
Title: DIPK2A promotes STX17- and VAMP7-mediated autophagosome-lysosome fusion by binding to VAMP7B.
Gene Copy Number Quantification of SHOX, VAMP7, and SRY for the Detection of Sex Chromosome Aneuploidies in Neonates.
Title: Gene Copy Number Quantification of SHOX, VAMP7, and SRY for the Detection of Sex Chromosome Aneuploidies in Neonates.
Cytotoxic Granule Exocytosis From Human Cytotoxic T Lymphocytes Is Mediated by VAMP7.
Title: Cytotoxic Granule Exocytosis From Human Cytotoxic T Lymphocytes Is Mediated by VAMP7.
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.

Submit: New GeneRIF Correction See all GeneRIFs (41)

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: 414 organisms have orthologs with human gene VAMP7
Orthologs

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
NOT involved_in autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium-ion regulated exocytosis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in endosome to lysosome transport	IDA Inferred from Direct Assay more info	PubMed
involved_in eosinophil degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in eosinophil degranulation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in natural killer cell degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neutrophil degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neutrophil degranulation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in phagocytosis, engulfment	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of histamine secretion by mast cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in vesicle fusion	IDA Inferred from Direct Assay more info	PubMed
involved_in vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
part_of SNARE complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in azurophil granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in integral component of membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in phagocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in phagocytic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in platelet alpha granule	IDA Inferred from Direct Assay more info	PubMed
located_in pseudopodium	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info

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

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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

cd14824
Location:27 → 75

Longin; longin domain
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 109.20211119

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

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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