VAPA VAMP associated protein A [Homo sapiens (human)] - Gene

Summary

Official Symbol: VAPAprovided by HGNC
Official Full Name: VAMP associated protein Aprovided by HGNC
Primary source: HGNC:HGNC:12648
See related: Ensembl:ENSG00000101558 MIM:605703; AllianceGenome:HGNC:12648
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: VAP-A; VAP33; VAMP-A; VAP-33; hVAP-33
Summary: The protein encoded by this gene is a type IV membrane protein. It is present in the plasma membrane and intracellular vesicles. It may also be associated with the cytoskeleton. This protein may function in vesicle trafficking, membrane fusion, protein complex assembly and cell motility. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in adrenal (RPKM 26.8), brain (RPKM 22.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 18p11.22

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (9914016..9960021)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (10077467..10123397)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (9914013..9960018)

Chromosome 18 - NC_000018.10 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?

VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites.
Title: VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites.
CircVAPA exerts oncogenic property in non-small cell lung cancer by the miR-876-5p/WNT5A axis.
Title: CircVAPA exerts oncogenic property in non-small cell lung cancer by the miR-876-5p/WNT5A axis.
Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.
Title: Sequence requirements of the FFAT-like motif for specific binding to VAP-A are revealed by NMR.
Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus.
Title: Role of Vesicle-Associated Membrane Protein-Associated Proteins (VAP) A and VAPB in Nuclear Egress of the Alphaherpesvirus Pseudorabies Virus.
CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
Title: CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
VAP proteins (VAPs) mediate ER to Golgi tethering and their loss may affect phosphatidylinositol-4-phosphate (PtdIns4P) transfer between these organelles. Loss of VAPs elevates PtdIns4P levels in the Golgi, leading to an expansion of the endosomal pool derived from the Golgi.
Title: VAMP associated proteins are required for autophagic and lysosomal degradation by promoting a PtdIns4P-mediated endosomal pathway.
Circular RNA VAPA is up-regulated in colorectal cancer and exerts oncogenic properties by sponging miR-101.
Title: Circular RNA circVAPA is up-regulated and exerts oncogenic properties by sponging miR-101 in colorectal cancer.
Thus, we characterized here MOSPD2, a novel tethering component related to VAP proteins(VAP-A and VAP-B), bridging the endoplasmic reticulum with a variety of distinct organelles.
Title: Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites.
The silencing of VAP-A or ORP3 abrogated the association of Rab7-positive late endosomes with nuclear envelope invaginations and, hence, the transport of endocytosed EV-derived components to the nucleoplasm of recipient cells.
Title: VAMP-associated protein-A and oxysterol-binding protein-related protein 3 promote the entry of late endosomes into the nucleoplasmic reticulum.
the component proteins of the machinery, OSBP, VAP, SAC1, and PITPNB, are all essential host factors for AiV replication. Importantly, the machinery is directly recruited to the RNA replication sites through previously unknown interactions of VAP/OSBP/SAC1 with the AiV proteins and with ACBD3.
Title: Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.

Submit: New GeneRIF Correction See all GeneRIFs (28)

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

EBI GWAS Catalog

Description
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope transmembrane glycoprotein gp41	env	HIV-1 gp41 is identified to have a physical interaction with VAMP (vesicle-associated membrane protein)-associated protein A (VAPA) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	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

D18S1196 (e-PCR)
- UniSTS:38146

D18S940E (e-PCR)
- UniSTS:150532

SHGC-32407 (e-PCR)
- UniSTS:18959

A006V14 (e-PCR)
- UniSTS:56613

D11S2560 (e-PCR)
- UniSTS:37928

RH92706 (e-PCR)
- UniSTS:84011

RH76596 (e-PCR)
- UniSTS:87126

SHGC-34906 (e-PCR)
- UniSTS:10639

RH35901 (e-PCR)
- UniSTS:54708

G20701 (e-PCR)
- UniSTS:54983

A006C24 (e-PCR)
- UniSTS:54984

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables FFAT motif binding	IBA Inferred from Biological aspect of Ancestor more info
enables FFAT motif binding	IDA Inferred from Direct Assay more info	PubMed
enables FFAT motif binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables cadherin binding	HDA more info	PubMed
enables microtubule binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle budding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ceramide transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in endoplasmic reticulum organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum-plasma membrane tethering	IDA Inferred from Direct Assay more info	PubMed
involved_in membrane fusion	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation by host of viral genome replication	IDA Inferred from Direct Assay more info	PubMed
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phospholipid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation by host of viral genome replication	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	HMP more info	PubMed
NOT involved_in protein folding in endoplasmic reticulum	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to endoplasmic reticulum	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingomyelin biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sterol transport	IDA Inferred from Direct Assay more info	PubMed
involved_in viral release from host cell	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in azurophil granule membrane	TAS Traceable Author Statement more info
colocalizes_with bicellular tight junction	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	HDA more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
NOT located_in endoplasmic reticulum exit site	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in microtubule cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
colocalizes_with perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor 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 vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vesicle-associated membrane protein-associated protein A

Names: 33 kDa VAMP-associated protein; VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa; epididymis secretory sperm binding protein

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_003574.6 → NP_003565.4 vesicle-associated membrane protein-associated protein A isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC006238, AF154847, BG488667, BP209270

Consensus CDS

CCDS11847.2

UniProtKB/Swiss-Prot

Q9P0L0

Related

ENSP00000345656.4, ENST00000340541.4

Conserved Domains (1) summary

pfam00635
Location:14 → 118

Motile_Sperm; MSP (Major sperm protein) domain
NM_194434.3 → NP_919415.2 vesicle-associated membrane protein-associated protein A isoform 2

See identical proteins and their annotated locations for NP_919415.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.

Source sequence(s)

AC006238, BC002992, BP209270

Consensus CDS

CCDS11848.2

UniProtKB/Swiss-Prot

A6NDZ0, D3DUI3, O75453, Q5U0E7, Q9P0L0, Q9UBZ2

Related

ENSP00000382880.3, ENST00000400000.7

Conserved Domains (1) summary

pfam00635
Location:14 → 118

Motile_Sperm; MSP (Major sperm protein) domain

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_000018.10 Reference GRCh38.p14 Primary Assembly

Range

9914016..9960021

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047437929.1 → XP_047293885.1 vesicle-associated membrane protein-associated protein A isoform X1
XM_047437932.1 → XP_047293888.1 vesicle-associated membrane protein-associated protein A isoform X2
XM_047437930.1 → XP_047293886.1 vesicle-associated membrane protein-associated protein A isoform X1
XM_017026079.2 → XP_016881568.1 vesicle-associated membrane protein-associated protein A isoform X2
XM_047437928.1 → XP_047293884.1 vesicle-associated membrane protein-associated protein A isoform X1
XM_047437931.1 → XP_047293887.1 vesicle-associated membrane protein-associated protein A isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060942.1 Alternate T2T-CHM13v2.0

Range

10077467..10123397

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054319357.1 → XP_054175332.1 vesicle-associated membrane protein-associated protein A isoform X2
XM_054319359.1 → XP_054175334.1 vesicle-associated membrane protein-associated protein A isoform X2
XM_054319355.1 → XP_054175330.1 vesicle-associated membrane protein-associated protein A isoform X2
XM_054319356.1 → XP_054175331.1 vesicle-associated membrane protein-associated protein A isoform X2
XM_054319353.1 → XP_054175328.1 vesicle-associated membrane protein-associated protein A isoform X1
XM_054319354.1 → XP_054175329.1 vesicle-associated membrane protein-associated protein A isoform X1
XM_054319358.1 → XP_054175333.1 vesicle-associated membrane protein-associated protein A isoform X2