VPS18 VPS18 core subunit of CORVET and HOPS complexes [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS18provided by HGNC
Official Full Name: VPS18 core subunit of CORVET and HOPS complexesprovided by HGNC
Primary source: HGNC:HGNC:15972
See related: Ensembl:ENSG00000104142 MIM:608551; AllianceGenome:HGNC:15972
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: PEP3
Summary: Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps18 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 7.7), kidney (RPKM 5.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q15.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (40894450..40903975)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (38700456..38709981)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (41186648..41196173)

Chromosome 15 - NC_000015.10 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?

Targeting of VPS18 by the lysosomotropic agent RDN reverses TFE3-mediated drug resistance.
Title: Targeting of VPS18 by the lysosomotropic agent RDN reverses TFE3-mediated drug resistance.
Study characterized the ubiquitinomes of Vps11/18 and demonstrated that these two factors are involved in the regulation of signal transduction by protein ubiquitination. VPS11/18 regulate several signaling factors and pathways, including Wnt, estrogen receptor alpha (ERalpha), and NFkappaB.
Title: Vps11 and Vps18 of Vps-C membrane traffic complexes are E3 ubiquitin ligases and fine-tune signalling.
VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction
Title: VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction.
Depletion of hVps18 or hMon2 reduced the efficient production of infectious HIV-1 virions in human cells.
Title: The cellular factors Vps18 and Mon2 are required for efficient production of infectious HIV-1 particles.
ubiquitin binding and ubiquitylation of GGA3-GAT domain are mutually inseparable through a ubiquitin ligase activity of hVPS18
Title: Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability.
hVPS18 may play an important role in regulation of SNK activity through its ubiquitin ligase
Title: Ubiquitylation and degradation of serum-inducible kinase by hVPS18, a RING-H2 type ubiquitin ligase.

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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

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. 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
Pr55(Gag)	gag	The CA domain of HIV-1 Gag and the clathrin heavy-chain repeat domain of VPS18 are required for the interaction between Gag and VPS18	PubMed
	gag	VPS18 and MON2 proteins are required for proper HIV-1 Gag localization to plasma membrane and the efficient production of infectious virions in human cells	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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in endosomal vesicle fusion	NAS Non-traceable Author Statement more info	PubMed
involved_in endosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysosome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of intracellular estrogen receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in organelle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of SNARE complex assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of synaptic vesicle exocytosis	EXP Inferred from Experiment more info	PubMed
involved_in regulation of synaptic vesicle exocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic vesicle exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in symbiont entry into host cell	IEA Inferred from Electronic Annotation more info
involved_in vesicle docking involved in exocytosis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of AP-3 adaptor complex	IEA Inferred from Electronic Annotation more info
part_of CORVET complex	NAS Non-traceable Author Statement more info	PubMed
part_of HOPS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HOPS complex	IDA Inferred from Direct Assay more info	PubMed
part_of HOPS complex	NAS Non-traceable Author Statement more info	PubMed
located_in actin filament	IEA Inferred from Electronic Annotation more info
located_in autophagosome	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
located_in early endosome	IEA Inferred from Electronic Annotation more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	TAS Traceable Author Statement more info
is_active_in glutamatergic synapse	EXP Inferred from Experiment more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 18 homolog

Names: VPS18, CORVET/HOPS core subunit; hVPS18; vacuolar protein sorting 18 homolog; vacuolar protein sorting protein 18

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_020857.3 → NP_065908.1 vacuolar protein sorting-associated protein 18 homolog

See identical proteins and their annotated locations for NP_065908.1

Status: REVIEWED

Source sequence(s)

AF308802, AL713725

Consensus CDS

CCDS10069.1

UniProtKB/Swiss-Prot

Q8TCG0, Q96DI3, Q9H268, Q9P253

Related

ENSP00000220509.5, ENST00000220509.10

Conserved Domains (3) summary

smart00299
Location:644 → 768

CLH; Clathrin heavy chain repeat homology

pfam00637
Location:644 → 769

Clathrin; Region in Clathrin and VPS

pfam05131
Location:291 → 434

Pep3_Vps18; Pep3/Vps18/deep orange family

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_000015.10 Reference GRCh38.p14 Primary Assembly

Range

40894450..40903975

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011521843.3 → XP_011520145.1 vacuolar protein sorting-associated protein 18 homolog isoform X1

Conserved Domains (3) summary

smart00299
Location:572 → 696

CLH; Clathrin heavy chain repeat homology

pfam00637
Location:572 → 697

Clathrin; Region in Clathrin and VPS

pfam05131
Location:219 → 362

Pep3_Vps18; Pep3/Vps18/deep orange family