VPS52 VPS52 subunit of GARP complex [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS52provided by HGNC
Official Full Name: VPS52 subunit of GARP complexprovided by HGNC
Primary source: HGNC:HGNC:10518
See related: Ensembl:ENSG00000223501 MIM:603443; AllianceGenome:HGNC:10518
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: ARE1; SAC2; SACM2L; dJ1033B10.5
Summary: This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Expression: Ubiquitous expression in thyroid (RPKM 15.7), testis (RPKM 14.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.32

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (33250272..33271965, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (33071634..33093327, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (33218049..33239742, complement)

Chromosome 6 - NC_000006.12 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?

The Sac2 operates upstream of granule docking, since loss of Sac2 prevented granule tethering to the plasma membrane and resulted in both reduced granule density and number of exocytic events.
Title: The PI(4)P phosphatase Sac2 controls insulin granule docking and release.
Loss of heterozygosity and stop-gain mutation of VPS52 were found in gastric cancer.
Title: VPS52 induces apoptosis via cathepsin D in gastric cancer.
These data demonstrate that the beneficial properties of SFN extend beyond activation of the KEAP1-Nrf2-ARE system and warrant further interrogation given the current use of this agent in multiple clinical trials
Title: Sulforaphane is a Nrf2-independent inhibitor of mitochondrial fission.
our data indicate that cisplatin resistance in HOCCs is partially attributable to their high expression of p62, which plays an important role in preventing ROS stress-induced apoptosis by regulating the Keap1-Nrf2-ARE signaling pathway.
Title: p62/SQSTM1 is involved in cisplatin resistance in human ovarian cancer cells via the Keap1-Nrf2-ARE system.
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.
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.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Susceptibility locus for non-obstructive azoospermia is localized within the HLA-DR/DQ subregion: primary role of DQB1*0604.
Observational study of gene-disease association. (HuGE Navigator)
Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
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.

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Phenotypes

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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

G19781 (e-PCR)
- UniSTS:45824

M2_2_3 (e-PCR)
- UniSTS:239159

RH10585 (e-PCR)
- UniSTS:88692

Sacm2l (e-PCR), detects polymorphism
- UniSTS:144359

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
enables syntaxin binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in ectodermal cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in embryonic ectodermal digestive tract development	IEA Inferred from Electronic Annotation more info
involved_in endocytic recycling	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytic recycling	NAS Non-traceable Author Statement more info	PubMed
involved_in lysosomal transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lysosomal transport	IDA Inferred from Direct Assay more info	PubMed
involved_in protein targeting	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	NAS Non-traceable Author Statement more info	PubMed
involved_in vesicle-mediated cholesterol transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of EARP complex	IDA Inferred from Direct Assay more info	PubMed
part_of EARP complex	IPI Inferred from Physical Interaction more info	PubMed
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 endosome membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in postsynapse	IEA Inferred from Electronic Annotation more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome	NAS Non-traceable Author Statement 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 52 homolog

Names: SAC2 suppressor of actin mutations 2-like protein; VPS52, GARP complex subunit; vacuolar protein sorting 52 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.

mRNA and Protein(s)

NM_001289174.2 → NP_001276103.1 vacuolar protein sorting-associated protein 52 homolog isoform 2

See identical proteins and their annotated locations for NP_001276103.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, initiates translation at an alternate start codon and lacks an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK093057, AK299563, BQ022405

UniProtKB/TrEMBL

B4DS44

Conserved Domains (1) summary

pfam04129
Location:27 → 534

Vps52; Vps52 / Sac2 family
NM_001289175.1 → NP_001276104.1 vacuolar protein sorting-associated protein 52 homolog isoform 3

See identical proteins and their annotated locations for NP_001276104.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which is shorter at the N-terminus, compared to isoform 1.

Source sequence(s)

AK001725, AK093057, AK297935, AK299563, BQ022405, DC395438

UniProtKB/TrEMBL

A0A1U9X8S4, B3KMF7

Conserved Domains (1) summary

pfam04129
Location:1 → 476

Vps52; Vps52 / Sac2 family
NM_001289176.1 → NP_001276105.1 vacuolar protein sorting-associated protein 52 homolog isoform 4

See identical proteins and their annotated locations for NP_001276105.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 4, which is shorter than isoform 1.

Source sequence(s)

AK001725, AK093057, AK299563, BQ022405, DC395438

UniProtKB/TrEMBL

B3KMF7

Related

ENST00000478934.5

Conserved Domains (1) summary

cl19950
Location:1 → 412

Sec3_C; Exocyst complex component Sec3
NM_022553.6 → NP_072047.4 vacuolar protein sorting-associated protein 52 homolog isoform 1

See identical proteins and their annotated locations for NP_072047.4

Status: REVIEWED

Description

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

Source sequence(s)

AK001725, BC040114, DC400338

Consensus CDS

CCDS4770.2

UniProtKB/Swiss-Prot

A2BF38, B0UZZ4, B4DNI9, Q53GR4, Q5JPA0, Q5SQW1, Q8IUN6, Q8N1B4, Q9NPT5

UniProtKB/TrEMBL

B4DS44, Q4VXZ2

Related

ENSP00000409952.2, ENST00000445902.3

Conserved Domains (1) summary

pfam04129
Location:94 → 601

Vps52; Vps52 / Sac2 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_000006.12 Reference GRCh38.p14 Primary Assembly

Range

33250272..33271965 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514799.2 → XP_011513101.1 vacuolar protein sorting-associated protein 52 homolog isoform X2

See identical proteins and their annotated locations for XP_011513101.1

UniProtKB/TrEMBL

B4DS44

Conserved Domains (1) summary

pfam04129
Location:27 → 534

Vps52; Vps52 / Sac2 family
XM_011514798.3 → XP_011513100.1 vacuolar protein sorting-associated protein 52 homolog isoform X2

See identical proteins and their annotated locations for XP_011513100.1

UniProtKB/TrEMBL

B4DS44

Conserved Domains (1) summary

pfam04129
Location:27 → 534

Vps52; Vps52 / Sac2 family
XM_011514797.2 → XP_011513099.1 vacuolar protein sorting-associated protein 52 homolog isoform X2

See identical proteins and their annotated locations for XP_011513099.1

UniProtKB/TrEMBL

B4DS44

Conserved Domains (1) summary

pfam04129
Location:27 → 534

Vps52; Vps52 / Sac2 family
XM_017011179.3 → XP_016866668.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

4661769..4683446 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329851.1 → XP_054185826.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054329849.1 → XP_054185824.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054329850.1 → XP_054185825.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054329852.1 → XP_054185827.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

4493784..4515479 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330334.1 → XP_054186309.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054330332.1 → XP_054186307.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054330333.1 → XP_054186308.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054330335.1 → XP_054186310.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

4669733..4671435 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

4686254..4707927 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330849.1 → XP_054186824.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054330848.1 → XP_054186823.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054330850.1 → XP_054186825.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054330851.1 → XP_054186826.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

4444672..4466382 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331111.1 → XP_054187086.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054331110.1 → XP_054187085.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054331112.1 → XP_054187087.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054331113.1 → XP_054187088.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

4698976..4720646 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331372.1 → XP_054187347.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054331371.1 → XP_054187346.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054331373.1 → XP_054187348.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054331374.1 → XP_054187349.1 vacuolar protein sorting-associated protein 52 homolog isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

33071634..33093327 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356196.1 → XP_054212171.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054356195.1 → XP_054212170.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054356197.1 → XP_054212172.1 vacuolar protein sorting-associated protein 52 homolog isoform X2
XM_054356198.1 → XP_054212173.1 vacuolar protein sorting-associated protein 52 homolog isoform X1