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VPS53 (VPS53, GARP complex subunit)

Identity

Alias_namesvacuolar protein sorting 53 (yeast)
vacuolar protein sorting 53 homolog (S. cerevisiae)
Alias_symbol (synonym)FLJ10979
HCCS1
Other aliasPCH2E
hVps53L
pp13624
HGNC (Hugo) VPS53
LocusID (NCBI) 55275
Atlas_Id 40589
Location 17p13.3  [Link to chromosome band 17p13]
Location_base_pair Starts at 508668 and ends at 714856 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ALDH1A3 (15q26.3) / VPS53 (17p13.3)SHB (9p13.2) / VPS53 (17p13.3)VPS53 (17p13.3) / GLOD4 (17p13.3)
VPS53 (17p13.3) / HS3ST5 (6q21)VPS53 (17p13.3) / MYH2 (17p13.1)VPS53 (17p13.3) / RTN4RL1 (17p13.3)
VPS53 (17p13.3) / STAT2 (12q13.3)VPS53 (17p13.3) / YWHAE (17p13.3)VPS53 (17p13.3) / ZZEF1 (17p13.2)
ALDH1A3 15q26.3 / VPS53 17p13.3VPS53 17p13.3 / GLOD4 17p13.3VPS53 17p13.3 / HS3ST5 6q21
VPS53 17p13.3 / MYH2 17p13.1VPS53 17p13.3 / RTN4RL1 17p13.3VPS53 17p13.3 / ZZEF1 17p13.2

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)VPS53   25608
Cards
Entrez_Gene (NCBI)VPS53  55275  VPS53, GARP complex subunit
AliasesHCCS1; PCH2E; hVps53L; pp13624
GeneCards (Weizmann)VPS53
Ensembl hg19 (Hinxton)ENSG00000141252 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000141252 [Gene_View]  chr17:508668-714856 [Contig_View]  VPS53 [Vega]
ICGC DataPortalENSG00000141252
TCGA cBioPortalVPS53
AceView (NCBI)VPS53
Genatlas (Paris)VPS53
WikiGenes55275
SOURCE (Princeton)VPS53
Genetics Home Reference (NIH)VPS53
Genomic and cartography
GoldenPath hg38 (UCSC)VPS53  -     chr17:508668-714856 -  17p13.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VPS53  -     17p13.3   [Description]    (hg19-Feb_2009)
EnsemblVPS53 - 17p13.3 [CytoView hg19]  VPS53 - 17p13.3 [CytoView hg38]
Mapping of homologs : NCBIVPS53 [Mapview hg19]  VPS53 [Mapview hg38]
OMIM615850   615851   
Gene and transcription
Genbank (Entrez)AF085927 AF246287 AF318335 AK001841 AK056323
RefSeq transcript (Entrez)NM_001128159 NM_018289
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VPS53
Cluster EST : UnigeneHs.461819 [ NCBI ]
CGAP (NCI)Hs.461819
Alternative Splicing GalleryENSG00000141252
Gene ExpressionVPS53 [ NCBI-GEO ]   VPS53 [ EBI - ARRAY_EXPRESS ]   VPS53 [ SEEK ]   VPS53 [ MEM ]
Gene Expression Viewer (FireBrowse)VPS53 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55275
GTEX Portal (Tissue expression)VPS53
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ5VIR6   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ5VIR6  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ5VIR6
Splice isoforms : SwissVarQ5VIR6
PhosPhoSitePlusQ5VIR6
Domains : Interpro (EBI)Vps53_N   
Domain families : Pfam (Sanger)Vps53_N (PF04100)   
Domain families : Pfam (NCBI)pfam04100   
Conserved Domain (NCBI)VPS53
DMDM Disease mutations55275
Blocks (Seattle)VPS53
SuperfamilyQ5VIR6
Human Protein AtlasENSG00000141252
Peptide AtlasQ5VIR6
HPRD07720
IPIIPI00181824   IPI00847977   IPI00889584   IPI00939440   IPI00889600   IPI00902942   IPI00656021   
Protein Interaction databases
DIP (DOE-UCLA)Q5VIR6
IntAct (EBI)Q5VIR6
FunCoupENSG00000141252
BioGRIDVPS53
STRING (EMBL)VPS53
ZODIACVPS53
Ontologies - Pathways
QuickGOQ5VIR6
Ontology : AmiGOGARP complex  protein binding  Golgi apparatus  trans-Golgi network  cytosol  lysosomal transport  endosome membrane  protein transport  membrane  endocytic recycling  trans-Golgi network membrane  retrograde transport, endosome to Golgi  perinuclear region of cytoplasm  recycling endosome  EARP complex  
Ontology : EGO-EBIGARP complex  protein binding  Golgi apparatus  trans-Golgi network  cytosol  lysosomal transport  endosome membrane  protein transport  membrane  endocytic recycling  trans-Golgi network membrane  retrograde transport, endosome to Golgi  perinuclear region of cytoplasm  recycling endosome  EARP complex  
NDEx NetworkVPS53
Atlas of Cancer Signalling NetworkVPS53
Wikipedia pathwaysVPS53
Orthology - Evolution
OrthoDB55275
GeneTree (enSembl)ENSG00000141252
Phylogenetic Trees/Animal Genes : TreeFamVPS53
HOVERGENQ5VIR6
HOGENOMQ5VIR6
Homologs : HomoloGeneVPS53
Homology/Alignments : Family Browser (UCSC)VPS53
Gene fusions - Rearrangements
Fusion : MitelmanALDH1A3/VPS53 [15q26.3/17p13.3]  [t(15;17)(q26;p13)]  
Fusion : MitelmanVPS53/GLOD4 [17p13.3/17p13.3]  [t(17;17)(p13;p13)]  
Fusion : MitelmanVPS53/HS3ST5 [17p13.3/6q21]  [t(6;17)(q22;p13)]  
Fusion : MitelmanVPS53/MYH2 [17p13.3/17p13.1]  [t(17;17)(p13;p13)]  
Fusion : MitelmanVPS53/RTN4RL1 [17p13.3/17p13.3]  [t(17;17)(p13;p13)]  
Fusion : MitelmanVPS53/ZZEF1 [17p13.3/17p13.2]  [t(17;17)(p13;p13)]  
Fusion: TCGAALDH1A3 15q26.3 VPS53 17p13.3 PRAD
Fusion: TCGAVPS53 17p13.3 GLOD4 17p13.3 LGG
Fusion: TCGAVPS53 17p13.3 HS3ST5 6q21 BRCA
Fusion: TCGAVPS53 17p13.3 MYH2 17p13.1 BRCA
Fusion: TCGAVPS53 17p13.3 RTN4RL1 17p13.3 BRCA
Fusion: TCGAVPS53 17p13.3 ZZEF1 17p13.2 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVPS53 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VPS53
dbVarVPS53
ClinVarVPS53
1000_GenomesVPS53 
Exome Variant ServerVPS53
ExAC (Exome Aggregation Consortium)VPS53 (select the gene name)
Genetic variants : HAPMAP55275
Genomic Variants (DGV)VPS53 [DGVbeta]
DECIPHERVPS53 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVPS53 
Mutations
ICGC Data PortalVPS53 
TCGA Data PortalVPS53 
Broad Tumor PortalVPS53
OASIS PortalVPS53 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVPS53  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVPS53
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch VPS53
DgiDB (Drug Gene Interaction Database)VPS53
DoCM (Curated mutations)VPS53 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VPS53 (select a term)
intoGenVPS53
Cancer3DVPS53(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM615850    615851   
Orphanet19511   
MedgenVPS53
Genetic Testing Registry VPS53
NextProtQ5VIR6 [Medical]
TSGene55275
GENETestsVPS53
Huge Navigator VPS53 [HugePedia]
snp3D : Map Gene to Disease55275
BioCentury BCIQVPS53
ClinGenVPS53
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55275
Chemical/Pharm GKB GenePA142670618
Clinical trialVPS53
Miscellaneous
canSAR (ICR)VPS53 (select the gene name)
Probes
Litterature
PubMed22 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVPS53
EVEXVPS53
GoPubMedVPS53
iHOPVPS53
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri May 19 12:43:54 CEST 2017

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