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 Ensembl:ENSG00000292366 MIM:300053; AllianceGenome:HGNC:11486
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
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (155881345..155943769)
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	Y	NC_000024.10 (57067865..57130289)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (154109337..154171772)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	Y	NC_060948.1 (62306325..62368760)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (155111008..155173433)
105.20220307	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?

The STX17-SNAP47-VAMP7/VAMP8 complex is the default SNARE complex mediating autophagosome-lysosome fusion.
Title: The STX17-SNAP47-VAMP7/VAMP8 complex is the default SNARE complex mediating autophagosome-lysosome fusion.
VAMP7j: A Splice Variant of Human VAMP7 That Modulates Neurite Outgrowth by Regulating L1CAM Transport to the Plasma Membrane.
Title: VAMP7j: A Splice Variant of Human VAMP7 That Modulates Neurite Outgrowth by Regulating L1CAM Transport to the Plasma Membrane.
The EMT-induced lncRNA NR2F1-AS1 positively modulates NR2F1 expression and drives gastric cancer via miR-29a-3p/VAMP7 axis.
Title: The EMT-induced lncRNA NR2F1-AS1 positively modulates NR2F1 expression and drives gastric cancer via miR-29a-3p/VAMP7 axis.
Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
Title: Role of VAMP7-Dependent Secretion of Reticulon 3 in Neurite Growth.
LINC00511 drives invasive behavior in hepatocellular carcinoma by regulating exosome secretion and invadopodia formation.
Title: LINC00511 drives invasive behavior in hepatocellular carcinoma by regulating exosome secretion and invadopodia formation.
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.

Submit: New GeneRIF Correction See all GeneRIFs (46)

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

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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

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
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
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
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
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
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 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_021435.2 RefSeqGene

Range

5002..67426

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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/TrEMBL

B4DE96

Related

ENSP00000427822.1, ENSP00000518619.1, ENST00000460621.6, ENST00000711265.1

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

Related

ENSP00000262640.6, ENSP00000518620.1, ENST00000262640.11, ENST00000711264.1

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, Q53GY7, Q7Z409, Q9H4A7

UniProtKB/TrEMBL

B2R6P4

Related

ENSP00000286448.6, ENSP00000518622.1, ENST00000286448.12, ENST00000711260.1

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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

155881345..155943769

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017029760.2 → XP_016885249.1 vesicle-associated membrane protein 7 isoform X2

UniProtKB/TrEMBL

B4DE96

Conserved Domains (2) summary

cd15871
Location:77 → 141

R-SNARE_VAMP7; SNARE motif of VAMP7

cd14824
Location:3 → 69

Longin; longin domain
XM_011531188.2 → 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.p14 Primary Assembly

Genomic

NC_000024.10 Reference GRCh38.p14 Primary Assembly

Range

57067865..57130289

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017030063.2 → XP_016885552.1 vesicle-associated membrane protein 7 isoform X2

UniProtKB/TrEMBL

B4DE96

Conserved Domains (2) summary

cd15871
Location:77 → 141

R-SNARE_VAMP7; SNARE motif of VAMP7

cd14824
Location:3 → 69

Longin; longin domain
XM_011545653.2 → 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

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

154109337..154171772

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054327627.1 → XP_054183602.1 vesicle-associated membrane protein 7 isoform X2
XM_054327626.1 → XP_054183601.1 vesicle-associated membrane protein 7 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060948.1 Alternate T2T-CHM13v2.0

Range

62306325..62368760

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054328325.1 → XP_054184300.1 vesicle-associated membrane protein 7 isoform X2
XM_054328324.1 → XP_054184299.1 vesicle-associated membrane protein 7 isoform X1
XM_054328323.1 → XP_054184298.1 vesicle-associated membrane protein 7 isoform X4

UniProtKB/Swiss-Prot

P51809, Q53GY7, Q7Z409, Q9H4A7
XM_054328322.1 → XP_054184297.1 vesicle-associated membrane protein 7 isoform X3