VAMP4 vesicle associated membrane protein 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VAMP4provided by HGNC
Official Full Name: vesicle associated membrane protein 4provided by HGNC
Primary source: HGNC:HGNC:12645
See related: Ensembl:ENSG00000117533 MIM:606909; AllianceGenome:HGNC:12645
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: VAMP-4; VAMP24
Summary: 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. The protein encoded by this gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. This protein may play a role in trans-Golgi network-to-endosome transport. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 9.9), testis (RPKM 7.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q24.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (171700160..171742065, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (171056627..171098537, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (171669300..171711205, complement)

Chromosome 1 - NC_000001.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

VAMP4 regulates insulin levels by targeting secretory granules to lysosomes.
Title: VAMP4 regulates insulin levels by targeting secretory granules to lysosomes.
Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinson's disease.
Title: Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinson's disease.
Syntaxin 6 and VAMP4 colocalize to the chlamydial inclusion.
Title: Vesicle-associated membrane protein 4 and syntaxin 6 interactions at the chlamydial inclusion.
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.
Data indicate that depletion of VAMP4, syntaxin 6, syntaxin 16, and Vti1a disrupted the Golgi ribbon structure.
Title: VAMP4 is required to maintain the ribbon structure of the Golgi apparatus.
colocalization of ATP11B with fluorescent cisplatin and with vesicular trafficking proteins, such as STX6 and VAMP4, strongly suggests that ATP11B contributes to secretory vesicular transport of cisplatin from Golgi to plasma membrane
Title: ATP11B mediates platinum resistance in ovarian cancer.
The findings of this study suggested that VAMP4 and syb2 diverge functionally, traffic independently and support distinct forms of neurotransmission
Title: VAMP4 directs synaptic vesicles to a pool that selectively maintains asynchronous neurotransmission.
VAMP7 is involved in many fusion processes and thus plays a more general function in NK-cell activity than VAMP4.
Title: VAMP4- and VAMP7-expressing vesicles are both required for cytotoxic granule exocytosis in NK cells.
Observational study of gene-disease association. (HuGE Navigator)
Title: Vesicle-associated membrane protein 4, a positional candidate gene on 1q24-q25, is not associated with type 2 diabetes in the Old Order Amish.

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G42281 (e-PCR)
- UniSTS:93954

G42285 (e-PCR)
- UniSTS:93958

SHGC-144585 (e-PCR)
- UniSTS:172295

G32422 (e-PCR)
- UniSTS:117009

SHGC-75917 (e-PCR)
- UniSTS:70702

SHGC-82902 (e-PCR)
- UniSTS:96091

RH102530 (e-PCR)
- UniSTS:96864

A009C32 (e-PCR)
- UniSTS:10115

D1S2351 (e-PCR)
- UniSTS:65686

D1S3031 (e-PCR)
- UniSTS:65687

AL034156 (e-PCR)
- UniSTS:93927

AL033823 (e-PCR)
- UniSTS:93688

D1S2532 (e-PCR)
- UniSTS:23807

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi ribbon formation	IEA Inferred from Electronic Annotation more info
involved_in SNARE complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in SNARE complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neurotransmitter receptor transport, endosome to postsynaptic membrane	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle endocytosis	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle to endosome fusion	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport in synapse	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	TAS Traceable Author Statement more info	PubMed
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in endosome	TAS Traceable Author Statement more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lysosome	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network membrane	TAS Traceable Author Statement more info
located_in transport vesicle	TAS Traceable Author Statement more info

General protein information

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Preferred Names: vesicle-associated membrane protein 4

Names: VAMP4/TAF3 fusion

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.

mRNA and Protein(s)

NM_001185127.2 → NP_001172056.1 vesicle-associated membrane protein 4 isoform 2

See identical proteins and their annotated locations for NP_001172056.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.

Source sequence(s)

BC007019, Z98751

Consensus CDS

CCDS53430.1

UniProtKB/Swiss-Prot

O75379

Related

ENSP00000356714.2, ENST00000367740.2

Conserved Domains (1) summary

cd15869
Location:49 → 115

R-SNARE_VAMP4; SNARE motif of VAMP4
NM_003762.5 → NP_003753.2 vesicle-associated membrane protein 4 isoform 1

See identical proteins and their annotated locations for NP_003753.2

Status: REVIEWED

Description

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

Source sequence(s)

AL035296, DB167275, Z98751

Consensus CDS

CCDS1298.1

UniProtKB/Swiss-Prot

A2IDD8, O75379, Q96IY9, Q96J20, Q9UEL7

UniProtKB/TrEMBL

A0A024R8Z6, Q6IAZ3

Related

ENSP00000236192.7, ENST00000236192.12

Conserved Domains (1) summary

cd15869
Location:50 → 116

R-SNARE_VAMP4; SNARE motif of VAMP4

RNA

NR_033704.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. This transcript is a candidate for nonsense-mediated mRNA decay is not thought to be translated.

Source sequence(s)

AK290441, DB167275, Z98751

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

171700160..171742065 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047433375.1 → XP_047289331.1 vesicle-associated membrane protein 4 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

171056627..171098537 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339395.1 → XP_054195370.1 vesicle-associated membrane protein 4 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_201994.1: Suppressed sequence

Description

NM_201994.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.