VPS52

gene
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Also known as ARE1

Summary

VPS52 (VPS52 subunit of GARP complex, HGNC:10518) is a protein-coding gene on chromosome 6p21.32, encoding Vacuolar protein sorting-associated protein 52 homolog (Q8N1B4). Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). It is a selective cancer dependency (DepMap: 30.3% of cell lines).

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.

Source: NCBI Gene 6293 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): complex neurodevelopmental disorder with or without congenital anomalies (Moderate, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 99 total
  • Cancer dependency (DepMap): dependent in 30.3% of screened cell lines
  • MANE Select transcript: NM_022553

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10518
Approved symbolVPS52
NameVPS52 subunit of GARP complex
Location6p21.32
Locus typegene with protein product
StatusApproved
AliasesARE1
Ensembl geneENSG00000223501
Ensembl biotypeprotein_coding
OMIM603443
Entrez6293

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 14 protein_coding, 6 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000445902, ENST00000461743, ENST00000463486, ENST00000464425, ENST00000471309, ENST00000478934, ENST00000482399, ENST00000493379, ENST00000493674, ENST00000495755, ENST00000495981, ENST00000865493, ENST00000865494, ENST00000865495, ENST00000865496, ENST00000865497, ENST00000865498, ENST00000865499, ENST00000920311, ENST00000954722, ENST00000954723, ENST00000954724, ENST00000954725

RefSeq mRNA: 4 — MANE Select: NM_022553 NM_001289174, NM_001289175, NM_001289176, NM_022553

CCDS: CCDS4770

Canonical transcript exons

ENST00000383210 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.1921 / max 87.0869, expressed in 1811 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
7311112.03681782
731105.59581705
731120.4149205
731090.144564

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lobe of thyroid glandUBERON:000111997.02gold quality
right uterine tubeUBERON:000130297.00gold quality
pituitary glandUBERON:000000796.78gold quality
metanephros cortexUBERON:001053396.67gold quality
right adrenal gland cortexUBERON:003582796.60gold quality
left lobe of thyroid glandUBERON:000112096.59gold quality
right adrenal glandUBERON:000123396.53gold quality
thyroid glandUBERON:000204696.46gold quality
right hemisphere of cerebellumUBERON:001489096.44gold quality
spleenUBERON:000210696.38gold quality
adenohypophysisUBERON:000219696.37gold quality
small intestine Peyer’s patchUBERON:000345496.19gold quality
cerebellar hemisphereUBERON:000224596.09gold quality
cerebellar cortexUBERON:000212996.08gold quality
cerebellumUBERON:000203796.05gold quality
left adrenal gland cortexUBERON:003582595.98gold quality
left adrenal glandUBERON:000123495.97gold quality
right ovaryUBERON:000211895.97gold quality
fundus of stomachUBERON:000116095.94gold quality
skin of abdomenUBERON:000141695.92gold quality
body of pancreasUBERON:000115095.90gold quality
left ovaryUBERON:000211995.86gold quality
tibial nerveUBERON:000132395.85gold quality
zone of skinUBERON:000001495.83gold quality
skin of legUBERON:000151195.82gold quality
body of stomachUBERON:000116195.73gold quality
lower esophagus mucosaUBERON:003583495.71gold quality
apex of heartUBERON:000209895.66gold quality
minor salivary glandUBERON:000183095.62gold quality
small intestineUBERON:000210895.61gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.83

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR, NFE2L2

miRNA regulators (miRDB)

28 targeting VPS52, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-6772-5P99.9467.01577
HSA-MIR-449399.9066.48977
HSA-MIR-427199.8868.322244
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-425599.7267.701541
HSA-MIR-182799.6368.573265
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-671-5P99.5267.111277
HSA-MIR-314799.5266.34388
HSA-MIR-616599.4467.121389
HSA-MIR-548V99.2969.471157
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-6768-3P99.1467.381319
HSA-MIR-6506-5P99.0465.661386
HSA-MIR-1304-5P98.9068.581054
HSA-MIR-619-5P98.5764.971988
HSA-MIR-4664-5P98.1765.071020
HSA-MIR-449497.8664.93850
HSA-MIR-6783-5P97.6767.211528
HSA-MIR-526B-5P97.4167.991074
HSA-MIR-342-5P97.2564.10817
HSA-MIR-397297.1966.46808
HSA-MIR-120297.1966.43827
HSA-MIR-451395.0467.06727
HSA-MIR-6855-3P95.0466.57725
HSA-MIR-6765-5P94.5162.65164

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 30.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 7)

  • 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. (PMID:15878329)
  • Missorting of cathepsin D in GARP-depleted cells results from accumulation of recycling MPRs in a population of light, small vesicles downstream of endosomes. (PMID:18367545)
  • 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] (PMID:19620288)
  • 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. (PMID:25269472)
  • 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 (PMID:27889639)
  • Loss of heterozygosity and stop-gain mutation of VPS52 were found in gastric cancer. (PMID:28791438)
  • 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. (PMID:31533953)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriovps52ENSDARG00000099258
mus_musculusVps52ENSMUSG00000024319
rattus_norvegicusVps52ENSRNOG00000000470
drosophila_melanogasterVps52FBGN0031710
caenorhabditis_elegansWBGENE00007059

Protein

Protein identifiers

Vacuolar protein sorting-associated protein 52 homologQ8N1B4 (reviewed: Q8N1B4)

Alternative names: SAC2 suppressor of actin mutations 2-like protein

All UniProt accessions (3): Q8N1B4, E9PI03, Q4VXZ2

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD. Acts as a component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane.

Subunit / interactions. Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54. Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin. EIPR1 interacts with both EARP and GARP complexes and mediates the recruitment of the GARP complex to the trans-Golgi network. Interacts with RAB6A and STX10. Interacts with BLTP3B.

Subcellular location. Golgi apparatus. trans-Golgi network membrane. Endosome membrane. Recycling endosome.

Similarity. Belongs to the VPS52 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N1B4-11yes
Q8N1B4-22

RefSeq proteins (4): NP_001276103, NP_001276104, NP_001276105, NP_072047* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007258Vps52Family
IPR048319Vps52_CCDomain
IPR048361Vps52_CDomain

Pfam: PF04129, PF20655

UniProt features (8 total): coiled-coil region 2, modified residue 2, initiator methionine 1, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N1B4-F186.100.61

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 2, 355

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6811440Retrograde transport at the Trans-Golgi-Network

MSigDB gene sets: 191 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GCM_MAP4K4, FREAC2_01, GOBP_LYSOSOMAL_TRANSPORT, GCM_GSPT1, GCANCTGNY_MYOD_Q6, MORF_HDAC1, GOBP_PROTEIN_TARGETING, GOBP_VACUOLAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, GOBP_ECTODERM_DEVELOPMENT, MORF_SKP1A

GO Biological Process (9): protein targeting (GO:0006605), Golgi to vacuole transport (GO:0006896), lysosomal transport (GO:0007041), ectodermal cell differentiation (GO:0010668), protein transport (GO:0015031), endocytic recycling (GO:0032456), retrograde transport, endosome to Golgi (GO:0042147), embryonic ectodermal digestive tract development (GO:0048611), vesicle-mediated cholesterol transport (GO:0090119)

GO Molecular Function (2): syntaxin binding (GO:0019905), protein binding (GO:0005515)

GO Cellular Component (12): GARP complex (GO:0000938), Golgi apparatus (GO:0005794), cytosol (GO:0005829), endosome membrane (GO:0010008), membrane (GO:0016020), trans-Golgi network membrane (GO:0032588), perinuclear region of cytoplasm (GO:0048471), recycling endosome (GO:0055037), presynapse (GO:0098793), postsynapse (GO:0098794), EARP complex (GO:1990745), endosome (GO:0005768)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Intra-Golgi and retrograde Golgi-to-ER traffic1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
cytoplasm3
establishment of protein localization2
vacuolar transport2
intercellular transport2
endosomal transport2
cytosolic transport2
cytoplasmic vesicle2
endomembrane system2
endosome2
synapse2
post-Golgi vesicle-mediated transport1
ectoderm development1
cell differentiation1
transport1
intracellular protein localization1
vesicle-mediated transport to the plasma membrane1
ectodermal digestive tract development1
embryonic digestive tract development1
vesicle-mediated transport1
intracellular cholesterol transport1
SNARE binding1
binding1
Golgi apparatus1
vesicle tethering complex1
intracellular membrane-bounded organelle1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
trans-Golgi network1
organelle membrane1
protein-containing complex1
recycling endosome1

Protein interactions and networks

STRING

1328 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VPS52VPS53Q5VIR6998
VPS52VPS54Q9P1Q0997
VPS52VPS51Q9UID3997
VPS52VPS50Q96JG6887
VPS52SOAT2O75908856
VPS52RPS18P25232846
VPS52COG3Q96JB2832
VPS52SOAT1P35610792
VPS52STX16O14662771
VPS52COG6Q9Y2V7758
VPS52EXOC1Q9NV70715
VPS52VTI1AQ96AJ9708
VPS52RAB6AP20340694
VPS52VAMP4O75379671
VPS52EXOC7Q9UPT5671

IntAct

497 interactions, top by confidence:

ABTypeScore
VPS50VPS53psi-mi:“MI:0914”(association)0.840
VPS52VPS50psi-mi:“MI:0915”(physical association)0.830
TXLNAVPS52psi-mi:“MI:0915”(physical association)0.780
VPS52RNF41psi-mi:“MI:0915”(physical association)0.780
VPS52TBC1D22Bpsi-mi:“MI:0915”(physical association)0.780
VPS52TXLNApsi-mi:“MI:0915”(physical association)0.780
RNF41VPS52psi-mi:“MI:0915”(physical association)0.780
TBC1D22BVPS52psi-mi:“MI:0915”(physical association)0.780
PSMC5PSMD11psi-mi:“MI:0914”(association)0.730
VPS52USP2psi-mi:“MI:0915”(physical association)0.720
VPS52DDX6psi-mi:“MI:0915”(physical association)0.720
MFAP1VPS52psi-mi:“MI:0915”(physical association)0.720
VPS52WTAPpsi-mi:“MI:0915”(physical association)0.720
TSTD2VPS52psi-mi:“MI:0915”(physical association)0.720
VPS52PPP1R18psi-mi:“MI:0915”(physical association)0.720
EPM2AIP1VPS52psi-mi:“MI:0915”(physical association)0.720
GOLGA1VPS52psi-mi:“MI:0915”(physical association)0.720
TSSK3VPS52psi-mi:“MI:0915”(physical association)0.720
TXN2VPS52psi-mi:“MI:0915”(physical association)0.720
AIRIMVPS52psi-mi:“MI:0915”(physical association)0.720
TRAF6VPS52psi-mi:“MI:0915”(physical association)0.720
ATP6V1DVPS52psi-mi:“MI:0915”(physical association)0.720
USP2VPS52psi-mi:“MI:0915”(physical association)0.720
DDX6VPS52psi-mi:“MI:0915”(physical association)0.720
VPS52MFAP1psi-mi:“MI:0915”(physical association)0.720

BioGRID (283): VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), VPS52 (Two-hybrid), TEAD4 (Two-hybrid), TPM3 (Two-hybrid), TRAF6 (Two-hybrid), LMO4 (Two-hybrid), STX11 (Two-hybrid)

ESM2 similar proteins: A1A4I4, A2SXS5, A6QQ47, B2DCZ9, O00255, O08908, O55166, O75146, O88559, P70268, Q0P5I0, Q0VCR8, Q155U0, Q16512, Q29RB1, Q2KJ58, Q3MHG0, Q3MII6, Q3SZI7, Q3UVL4, Q4V9Y0, Q505L3, Q5R7R6, Q5TJF0, Q5ZJ25, Q63433, Q63788, Q68FF6, Q68FP9, Q69Z89, Q6PB44, Q6ZT62, Q865S3, Q8BI71, Q8BZQ7, Q8C190, Q8C754, Q8N1B4, Q8R1U1, Q8R3I3

Diamond homologs: G5EFV8, O55166, Q5TJF0, Q8C754, Q8N1B4, Q94KD3, Q9FVV6

SIGNOR signaling

1 interactions.

AEffectBMechanism
RNF41“down-regulates quantity by destabilization”VPS52ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 81 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Retrograde transport at the Trans-Golgi-Network522.0×1e-03
AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274)519.4×1e-03

GO biological processes:

GO termPartnersFoldFDR
endocytic recycling727.1×3e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

99 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance67
Likely benign0
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3326 predictions. Top by Δscore:

VariantEffectΔscore
6:33251855:CATA:Cdonor_loss1.0000
6:33251856:ATACC:Adonor_loss1.0000
6:33251857:TACC:Tdonor_loss1.0000
6:33251858:A:Cdonor_loss1.0000
6:33251859:C:Gdonor_loss1.0000
6:33251968:ATTCC:Aacceptor_loss1.0000
6:33251969:TTCC:Tacceptor_loss1.0000
6:33251970:TCCT:Tacceptor_loss1.0000
6:33251971:CCTGG:Cacceptor_loss1.0000
6:33251973:T:Gacceptor_loss1.0000
6:33263545:CGCTC:Cacceptor_gain1.0000
6:33263547:CTC:Cacceptor_gain1.0000
6:33263548:TC:Tacceptor_gain1.0000
6:33263548:TCCT:Tacceptor_loss1.0000
6:33263549:CC:Cacceptor_gain1.0000
6:33263550:C:CCacceptor_gain1.0000
6:33263550:CT:Cacceptor_loss1.0000
6:33263786:G:Cdonor_gain1.0000
6:33263828:T:TAdonor_gain1.0000
6:33263881:T:Cacceptor_loss1.0000
6:33264398:C:Adonor_gain1.0000
6:33264801:C:Adonor_gain1.0000
6:33266616:C:CTacceptor_gain1.0000
6:33267646:AAGG:Adonor_gain1.0000
6:33267736:CATA:Cacceptor_gain1.0000
6:33267740:C:CCacceptor_gain1.0000
6:33267859:CCTTA:Cdonor_loss1.0000
6:33267860:CTTAC:Cdonor_loss1.0000
6:33267862:TAC:Tdonor_loss1.0000
6:33267863:ACCTG:Adonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000532472 (6:33257018 G>T), RS1000730962 (6:33264492 C>G,T), RS1000779401 (6:33250292 A>G), RS1000807229 (6:33269923 A>C), RS1001184413 (6:33264132 C>G), RS1001799027 (6:33255919 G>C,T), RS1001899236 (6:33263939 G>A), RS1002011 (6:33250460 G>A), RS1002076048 (6:33270403 T>G), RS1002583131 (6:33259973 A>C,T), RS1002628716 (6:33260961 T>C), RS1002696843 (6:33273466 GTCT>G,GTCTTCT), RS1002727320 (6:33267014 G>A), RS1002733868 (6:33267625 G>A), RS1002807468 (6:33273686 C>T)

Disease associations

OMIM: gene MIM:603443 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
complex neurodevelopmental disorder with or without congenital anomaliesModerateAutosomal recessive

Mondo (1): complex neurodevelopmental disorder with or without congenital anomalies (MONDO:0100465)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004521_287Autism spectrum disorder or schizophrenia5.000000e-08
GCST005951_153Body mass index5.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects expression, affects cotreatment6
bisphenol Adecreases expression2
Benzo(a)pyreneaffects methylation, decreases methylation2
bisphenol Faffects cotreatment, increases expression1
dicrotophosincreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
tetrabromobisphenol Adecreases expression1
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
dorsomorphindecreases expression, affects cotreatment1
pentabrominated diphenyl ether 100increases expression1
hexabrominated diphenyl ether 153increases expression1
(+)-JQ1 compounddecreases expression1
Vorinostatdecreases expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Cisplatinaffects response to substance1
Dexamethasoneaffects cotreatment, increases expression1
Fluorouracildecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Methapyrilenedecreases methylation1
Thiramdecreases expression1
Tretinoinincreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_TX68HAP1 VPS52 (-) 1Cancer cell lineMale
CVCL_TX69HAP1 VPS52 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.