Gene: VPS54

51542
HCC8|PPP1R164|SLP-8p|VPS54L|WR|hVps54L
VPS54, GARP complex subunit
protein-coding
2p15-p14
Ensembl:ENSG00000143952 MIM:614633 Vega:OTTHUMG00000152627 UniprotKB:Q9P1Q0
NG_042277.1
SNP Mapped
2   ANCO-SNPs
AD
0   
NA (AD)  NA (ND)   (Frontal_Cortex)
6.680e-1 (AD)  5.862e-1 (ND)

ANCO-SNPs

SNP ID Position Alleles Trait Variation Type
rs13009774chr2:63977706 (GRCh38.p7)T>Galcohol dependenceSNV(Single Nucleotide Variation)
rs1345479chr2:63903097 (GRCh38.p7)A>Galcohol dependenceSNV(Single Nucleotide Variation)

DNA Methylation

There is no related methylation information for this gene.

Gene Expression in Different Tissues

Temporal and Spatial Expressions (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes average value of the expressions.

Top Co-expressed Genes in Brain-Frontal Cortex (BA9) (GTEx v7)

Top 10 positively co-expressed genes

Gene Symbol Pearson Correlation Coefficient
PRPF40A0.89
PAK20.864
OSBPL90.864
ZNF1460.849
RAP1A0.848
DICER10.846
TRMT130.845
ELK40.844
SOS20.844
PRPF38B0.843

Top 10 negatively co-expressed genes

Gene Symbol Pearson Correlation Coefficient
OR4F29-0.509
OR4F5-0.467
SHISA8-0.326
CHRNA2-0.322
CRH-0.313
GGN-0.312
KCNG1-0.309
ADRA1D-0.293
GSG1-0.293
PRTN3-0.291

Drugs/Compounds

    There is no DrugBank record for this gene !

ID Drug Name Action PubMed
D000082AcetaminophenAcetaminophen results in decreased expression of VPS54 mRNA21420995
D000082AcetaminophenAcetaminophen affects the expression of VPS54 mRNA17562736
C014949acetylhydrazineacetylhydrazine results in decreased expression of VPS54 mRNA15282401
D016604Aflatoxin B1Aflatoxin B1 results in increased expression of VPS54 mRNA19770486
D000643Ammonium ChlorideAmmonium Chloride affects the expression of VPS54 mRNA16483693
D001151ArsenicArsenic affects the methylation of VPS54 gene25304211
D0151237,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide"7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide results in decreased expression of VPS54 mRNA"19150397
C006780bisphenol Abisphenol A affects the expression of VPS54 mRNA21786754
C006780bisphenol Abisphenol A results in increased expression of VPS54 mRNA25181051
C006780bisphenol Abisphenol A results in increased methylation of VPS54 gene28505145
D019327Copper SulfateCopper Sulfate results in decreased expression of VPS54 mRNA19549813
D016572CyclosporineCyclosporine results in decreased expression of VPS54 mRNA25562108
C000944dicrotophosdicrotophos results in decreased expression of VPS54 mRNA28302478
C045651epigallocatechin gallate[potassium chromate(VI) co-treated with epigallocatechin gallate] results in decreased expression of VPS54 mRNA22079256
D005557FormaldehydeFormaldehyde results in decreased expression of VPS54 mRNA23649840
D006861Hydrogen PeroxideHydrogen Peroxide results in increased expression of VPS54 mRNA26846883
D006861Hydrogen PeroxideHydrogen Peroxide results in increased expression of VPS54 mRNA18951874
D006997Hypochlorous AcidHypochlorous Acid results in increased expression of VPS54 mRNA19376150
D015759Ionomycin[Tetradecanoylphorbol Acetate co-treated with Ionomycin] results in decreased expression of VPS54 mRNA25613284
C544151jinfukangjinfukang results in decreased expression of VPS54 mRNA27392435
C523184mocetinostatmocetinostat results in increased expression of VPS54 mRNA27255383
D037742Nanotubes, Carbon"Nanotubes, Carbon analog results in decreased expression of VPS54 mRNA"25554681
D010936Plant ExtractsPlant Extracts results in increased expression of VPS54 mRNA23557933
C027373potassium chromate(VI)[potassium chromate(VI) co-treated with epigallocatechin gallate] results in decreased expression of VPS54 mRNA22079256
C027373potassium chromate(VI)potassium chromate(VI) results in decreased expression of VPS54 mRNA22079256
D011374ProgesteroneProgesterone inhibits the reaction [VPS54 gene mutant form results in decreased activity of CHAT protein]17052708
D011374ProgesteroneProgesterone inhibits the reaction [VPS54 gene mutant form results in decreased expression of BDNF mRNA]17052708
D011374ProgesteroneProgesterone inhibits the reaction [VPS54 gene mutant form results in decreased expression of CHAT protein]17052708
D011374ProgesteroneProgesterone inhibits the reaction [VPS54 mutant form results in decreased expression of CHAT protein]19693665
D011374ProgesteroneProgesterone inhibits the reaction [VPS54 mutant form results in increased expression of GAP43 mRNA]19693665
D011794QuercetinQuercetin results in decreased expression of VPS54 mRNA21632981
D012822Silicon DioxideSilicon Dioxide results in decreased expression of VPS54 mRNA19073995
C009277sodium arsenatesodium arsenate results in increased expression of VPS54 mRNA21795629
D013755Tetradecanoylphorbol Acetate[Tetradecanoylphorbol Acetate co-treated with Ionomycin] results in decreased expression of VPS54 mRNA25613284
C012589trichostatin Atrichostatin A affects the expression of VPS54 mRNA28542535
D014635Valproic AcidValproic Acid results in increased expression of VPS54 mRNA29154799
D001335Vehicle EmissionsVehicle Emissions affects the methylation of VPS54 gene25560391

GO/Pathway

GO ID GO Term Qualifier Evidence PubMed
GO:0005515protein binding-IPI15878329  20685960  
GO:0019905syntaxin binding-IBA21873635  
GO ID GO Term Qualifier Evidence PubMed
GO:0006896Golgi to vacuole transport-IBA21873635  
GO:0007041lysosomal transport-IMP25799061  
GO:0015031protein transport-IEA-  
GO:0042147retrograde transport, endosome to Golgi-IBA21873635  
GO:0042147retrograde transport, endosome to Golgi-IMP25799061  
GO:0048873homeostasis of number of cells within a tissue-IEA-  
GO:0050881musculoskeletal movement-IEA-  
GO:0060052neurofilament cytoskeleton organization-IEA-  
GO ID GO Term Qualifier Evidence PubMed
GO:0000938GARP complex-IBA21873635  
GO:0000938GARP complex-IDA19620288  25799061  
GO:0005654nucleoplasm-IDA-  
GO:0005794Golgi apparatus-IDA15878329  
GO:0005802trans-Golgi network-IDA25799061  
GO:0005802trans-Golgi network-IMP25795912  
GO:0005829cytosol-IEA-  
GO:0032588trans-Golgi network membrane-TAS-  
GO:0048471perinuclear region of cytoplasm-IDA15878329  
KEGG ID KEGG Term
Reactome ID Reactome Term Evidence
R-HSA-199991Membrane TraffickingTAS
R-HSA-5653656Vesicle-mediated transportTAS
R-HSA-6811440Retrograde transport at the Trans-Golgi-NetworkTAS
R-HSA-6811442Intra-Golgi and retrograde Golgi-to-ER trafficTAS

Interactions (STRING v10.5, Interaction Score >= 0.400)

Publications (Co-occurrence of gene symbol strings and ANCO-Dependence terms)

PMID Title (Year) Author Journal