VPS54 VPS54 subunit of GARP complex [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS54provided by HGNC
Official Full Name: VPS54 subunit of GARP complexprovided by HGNC
Primary source: HGNC:HGNC:18652
See related: Ensembl:ENSG00000143952 MIM:614633; AllianceGenome:HGNC:18652
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: WR; HCC8; SLP-8p; VPS54L; hVps54L; PPP1R164
Summary: This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 11.2), prostate (RPKM 10.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p15-p14

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (63892150..64019428, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (63899706..64027065, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (64119284..64246562, complement)

Chromosome 2 - NC_000002.12 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 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?

This study suggests that VPS54 mutations are not a common cause of Amyotrophic Lateral Sclerosis in Italian population
Title: VPS54 genetic analysis in ALS Italian cohort.
Golgi-associated retrograde protein orchestrates retrograde transport from endosomes to the trans-Golgi network by promoting vesicle tethering and assembly of SNARE complexes in consecutive, independent steps.[Golgi associated retrograde protein]
Title: Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network.
Severely reduced levels of mutant Vps54 and, consequently, of the whole GARP complex underlie the phenotype of the wobbler mouse.
Title: Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Missorting of cathepsin D in GARP-depleted cells results from accumulation of recycling MPRs in a population of light, small vesicles downstream of endosomes.
Title: Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes.
mutations in VPS54 are not a major cause of ALS (amyotrophic lateral sclerosis)
Title: Evaluation of the Golgi trafficking protein VPS54 (wobbler) as a candidate for ALS.
Observational study of gene-disease association. (HuGE Navigator)
Title: Evaluation of the Golgi trafficking protein VPS54 (wobbler) as a candidate for ALS.
Golgi associated retrograde protein complex, consisting of the Vps52, Vps53, and Vps54 proteins, shows significant conservation between various species but diversification and specialization result in important differences in human cells.
Title: Characterization of the human GARP (Golgi associated retrograde protein) complex.
PMID:12039048 mostly pertains to mouse and rat but contains some general comments about the structure and function of Vps54 homolog in other species, including human.
Title: Identification, characterization and cytogenetic mapping of a yeast Vps54 homolog in rat and mouse.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. 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

RH93801 (e-PCR)
- UniSTS:90948

RH46124 (e-PCR)
- UniSTS:47238

D2S147 (e-PCR)
- UniSTS:7381

NoName (e-PCR)
- UniSTS:236530

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 Golgi to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-glutamate import	IEA Inferred from Electronic Annotation more info
involved_in apoptotic DNA fragmentation	IEA Inferred from Electronic Annotation more info
involved_in astrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to progesterone stimulus	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells within a tissue	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lysosomal transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in microglia differentiation	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
involved_in motor behavior	IEA Inferred from Electronic Annotation more info
involved_in motor neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in musculoskeletal movement	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of motor neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in neural tissue regeneration	IEA Inferred from Electronic Annotation more info
involved_in neurofilament cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in neuroinflammatory response	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in neuron projection morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein targeting to ER	IEA Inferred from Electronic Annotation more info
involved_in protein targeting to lysosome	IEA Inferred from Electronic Annotation more info
involved_in regulation of growth	IEA Inferred from Electronic Annotation more info
involved_in respiratory electron transport chain	IEA Inferred from Electronic Annotation more info
involved_in response to antibiotic	IEA Inferred from Electronic Annotation more info
involved_in response to calcium ion	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	NAS Non-traceable Author Statement more info	PubMed
involved_in skeletal muscle tissue growth	IEA Inferred from Electronic Annotation more info
involved_in spermatid differentiation	IEA Inferred from Electronic Annotation more info
involved_in sphingolipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in striated muscle contraction	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, GABAergic	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info
involved_in thrombin-activated receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin recycling	IEA Inferred from Electronic Annotation more info
involved_in vacuole organization	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated cholesterol transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of GARP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of GARP complex	IDA Inferred from Direct Assay more info	PubMed
part_of GARP complex	NAS Non-traceable Author Statement more info	PubMed
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	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 trans-Golgi network	IMP Inferred from Mutant Phenotype more info	PubMed
located_in trans-Golgi network membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 54

Names: VPS54, GARP complex subunit; hepatocellular carcinoma protein 8; protein phosphatase 1, regulatory subunit 164; tumor antigen HOM-HCC-8; tumor antigen SLP-8p; vacuolar protein sorting 54 homolog

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_042277.1 RefSeqGene

Range

4653..131931

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001005739.2 → NP_001005739.1 vacuolar protein sorting-associated protein 54 isoform 2

See identical proteins and their annotated locations for NP_001005739.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in one of the 5' coding exons compared to transcript variant 1, resulting in a shorter isoform (2) compared to isoform 1.

Source sequence(s)

AC092588, AK002205, AL514510, AW452246, BC030275, BC041868

Consensus CDS

CCDS46302.1

UniProtKB/TrEMBL

A8KA24

Related

ENSP00000386980.3, ENST00000409558.8

Conserved Domains (1) summary

pfam07928
Location:725 → 855

Vps54; Vps54-like protein
NM_016516.3 → NP_057600.2 vacuolar protein sorting-associated protein 54 isoform 1

See identical proteins and their annotated locations for NP_057600.2

Status: REVIEWED

Description

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

Source sequence(s)

AC092588, AF102177, AK002205, AL514510, AW452246, BC030275, BC041868

Consensus CDS

CCDS33208.1

UniProtKB/Swiss-Prot

Q5VIR5, Q86YF7, Q8N6G3, Q9NPV0, Q9NT07, Q9NUJ0, Q9P1Q0

UniProtKB/TrEMBL

A8K9F4

Related

ENSP00000272322.4, ENST00000272322.9

Conserved Domains (1) summary

pfam07928
Location:737 → 867

Vps54; Vps54-like protein

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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

63892150..64019428 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017004316.2 → XP_016859805.1 vacuolar protein sorting-associated protein 54 isoform X3

UniProtKB/TrEMBL

A8KA24

Related

ENSP00000346499.3, ENST00000354504.7
XM_047444728.1 → XP_047300684.1 vacuolar protein sorting-associated protein 54 isoform X1

UniProtKB/Swiss-Prot

Q5VIR5, Q86YF7, Q8N6G3, Q9NPV0, Q9NT07, Q9NUJ0, Q9P1Q0
XM_047444730.1 → XP_047300686.1 vacuolar protein sorting-associated protein 54 isoform X3
XM_047444727.1 → XP_047300683.1 vacuolar protein sorting-associated protein 54 isoform X1

UniProtKB/Swiss-Prot

Q5VIR5, Q86YF7, Q8N6G3, Q9NPV0, Q9NT07, Q9NUJ0, Q9P1Q0
XM_047444729.1 → XP_047300685.1 vacuolar protein sorting-associated protein 54 isoform X2
XM_047444731.1 → XP_047300687.1 vacuolar protein sorting-associated protein 54 isoform X4
XM_047444732.1 → XP_047300688.1 vacuolar protein sorting-associated protein 54 isoform X5

RNA

XR_007076389.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

63899706..64027065 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054342521.1 → XP_054198496.1 vacuolar protein sorting-associated protein 54 isoform X3
XM_054342519.1 → XP_054198494.1 vacuolar protein sorting-associated protein 54 isoform X1

UniProtKB/Swiss-Prot

Q5VIR5, Q86YF7, Q8N6G3, Q9NPV0, Q9NT07, Q9NUJ0, Q9P1Q0
XM_054342522.1 → XP_054198497.1 vacuolar protein sorting-associated protein 54 isoform X3
XM_054342520.1 → XP_054198495.1 vacuolar protein sorting-associated protein 54 isoform X2
XM_054342523.1 → XP_054198498.1 vacuolar protein sorting-associated protein 54 isoform X4
XM_054342524.1 → XP_054198499.1 vacuolar protein sorting-associated protein 54 isoform X5