VAMP1 vesicle associated membrane protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VAMP1provided by HGNC
Official Full Name: vesicle associated membrane protein 1provided by HGNC
Primary source: HGNC:HGNC:12642
See related: Ensembl:ENSG00000139190 MIM:185880; AllianceGenome:HGNC:12642
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: SAX1; SYB1; CMS25; SPAX1; VAMP-1
Summary: Synapotobrevins, syntaxins, and the 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. Mutations in this gene are associated with autosomal dominant spastic ataxia 1. Multiple alternative splice variants have been described, but the full-length nature of some variants has not been defined. [provided by RefSeq, Jul 2014]
Expression: Broad expression in bone marrow (RPKM 21.7), lymph node (RPKM 20.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6462237..6470677, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6472621..6481015, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (6571403..6579843, complement)

Chromosome 12 - NC_000012.12 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?

Expanding the genetic and phenotypic spectrum of congenital myasthenic syndrome: new homozygous VAMP1 splicing variants in 2 novel individuals.
Title: Expanding the genetic and phenotypic spectrum of congenital myasthenic syndrome: new homozygous VAMP1 splicing variants in 2 novel individuals.
locus for autosomal dominant hereditary spastic ataxia, SAX1, maps to chromosome 12p
Title: A locus for autosomal dominant hereditary spastic ataxia, SAX1, maps to chromosome 12p13.
Prefrontal cortex VAMP1 gene network moderates the effect of the early environment on cognitive flexibility in children.
Title: Prefrontal cortex VAMP1 gene network moderates the effect of the early environment on cognitive flexibility in children.
Recessive VAMP1 mutations associated with severe congenital myasthenic syndromes - A recognizable clinical phenotype.
Title: Recessive VAMP1 mutations associated with severe congenital myasthenic syndromes - A recognizable clinical phenotype.
VAMP1 homozygous mutations causes of presynaptic congenital myasthenic syndrome.
Title: Homozygous mutations in VAMP1 cause a presynaptic congenital myasthenic syndrome.
residue 48 of VAMP1 varies frequently between M and I across seventeen closely related primate species, suggesting a potential selective pressure from members of BoNTs for resistance in vertebrates.
Title: Widespread sequence variations in VAMP1 across vertebrates suggest a potential selective pressure from botulinum neurotoxins.
Genetically regulated VAMP1 expression in the brain may modify both Alzheimer's disease risk and may contribute to Alzheimer's pathophysiology
Title: Genetically-controlled Vesicle-Associated Membrane Protein 1 expression may contribute to Alzheimer's pathophysiology and susceptibility.
This report identifies vesicle-associated membrane protein 1 (VAMP1), which encodes a critical protein for synaptic exocytosis, as the responsible gene fora dominantly inherited spastic ataxia
Title: VAMP1 mutation causes dominant hereditary spastic ataxia in Newfoundland families.
multiple domains outside the R-SNARE of tomosyn are critical to the efficacy of inhibition by tomosyn on exocytotic secretion
Title: Structural and functional analysis of tomosyn identifies domains important in exocytotic regulation.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Myasthenic syndrome, congenital, 25, presynaptic MedGen: C5193027 OMIM: 618323 GeneReviews: Not available	not available
Spastic ataxia 1 MedGen: C1970107 OMIM: 108600 GeneReviews: Hereditary Ataxia Overview	not available

EBI GWAS Catalog

Description
Genome-wide association with bone mass and geometry in the Framingham Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D12S111E (e-PCR)
- UniSTS:71946

G41275 (e-PCR)
- UniSTS:49430

GDB:214816 (e-PCR)
- UniSTS:156186

D12S1215E (e-PCR)
- UniSTS:67928

RH80806 (e-PCR)
- UniSTS:90978

STS-M36200 (e-PCR)
- UniSTS:35229

D12S900 (e-PCR)
- UniSTS:149920

GDB:384731 (e-PCR)
- UniSTS:157090

RH44502 (e-PCR)
- UniSTS:75946

D12S111E (e-PCR)
- UniSTS:147401

D12S111E (e-PCR)
- UniSTS:74445

VAMP1_2267 (e-PCR)
- UniSTS:281073

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in SNARE complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
NOT located_in azurophil granule membrane	IDA Inferred from Direct Assay more info	PubMed
NOT located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in mitochondrial outer membrane	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in specific granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	TAS Traceable Author Statement more info
located_in tertiary granule membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vesicle-associated membrane protein 1

Names: spastic ataxia 1 (autosomal dominant); vesicle-associated membrane protein 1 (synaptobrevin 1)

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_042188.2 RefSeqGene

Range

5223..13663

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001297438.2 → NP_001284367.1 vesicle-associated membrane protein 1 isoform 4

See identical proteins and their annotated locations for NP_001284367.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1. Isoforms 3 and 4 are the same length but differ in their C-termini.

Source sequence(s)

AC005840

Consensus CDS

CCDS73422.1

UniProtKB/TrEMBL

A8K0D3, F5GZV7

Related

ENSP00000444181.1, ENST00000535180.5

Conserved Domains (1) summary

cd15870
Location:32 → 94

R-SNARE_VAMP2; SNARE motif of VAMP2
NM_014231.5 → NP_055046.1 vesicle-associated membrane protein 1 isoform 1

See identical proteins and their annotated locations for NP_055046.1

Status: REVIEWED

Description

Transcript Variant: This variant (1), also known as VAMP-1A, encodes the longest isoform (1).

Source sequence(s)

AC005840

Consensus CDS

CCDS41740.1

UniProtKB/Swiss-Prot

A8MVP3, D3DUR3, O75468, P23763, Q15857, Q6FG94, Q8IVC9

UniProtKB/TrEMBL

A8K0D3

Related

ENSP00000379602.3, ENST00000396308.4

Conserved Domains (1) summary

cd15870
Location:32 → 94

R-SNARE_VAMP2; SNARE motif of VAMP2
NM_016830.4 → NP_058439.1 vesicle-associated membrane protein 1 isoform 3

See identical proteins and their annotated locations for NP_058439.1

Status: REVIEWED

Description

Transcript Variant: This variant (3), also known as VAMP-1B, contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1. Isoforms 3 and 4 are the same length but differ in their C-termini.

Source sequence(s)

AC005840

Consensus CDS

CCDS44809.1

UniProtKB/TrEMBL

A8K0D3

Related

ENSP00000383702.3, ENST00000400911.7

Conserved Domains (1) summary

cd15870
Location:32 → 94

R-SNARE_VAMP2; SNARE motif of VAMP2
NM_199245.3 → NP_954740.1 vesicle-associated membrane protein 1 isoform 2

See identical proteins and their annotated locations for NP_954740.1

Status: REVIEWED

Description

Transcript Variant: This variant (2), also known as VAMP-1D, has a different 3' structure, resulting in a novel 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AC005840

Consensus CDS

CCDS31731.1

UniProtKB/TrEMBL

A8K0D3

Related

ENSP00000355122.3, ENST00000361716.8

Conserved Domains (1) summary

cd15870
Location:32 → 94

R-SNARE_VAMP2; SNARE motif of VAMP2

RNA

NR_123717.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate internal exon and contains an alternate 3' terminal 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)

AC005840