Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

VPS54 (VPS54, GARP complex subunit)

Identity

Alias_namesregulatory subunit 164
Alias_symbol (synonym)HCC8
PPP1R164
Other aliasSLP-8p
VPS54L
WR
hVps54L
HGNC (Hugo) VPS54
LocusID (NCBI) 51542
Atlas_Id 42798
Location 2p15  [Link to chromosome band 2p15]
Location_base_pair Starts at 63892533 and ends at 64019080 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
PIWIL2 (8p21.3) / VPS54 (2p14)SPECC1 (17p11.2) / VPS54 (2p14)VPS54 (2p14) / ANKHD1 (5q31.3)
VPS54 (2p14) / PELI1 (2p14)VPS54 (2p14) / RBPMS2 (15q22.31)WDPCP (2p15) / VPS54 (2p14)
VPS54 2p14 / PELI1 2p14WDPCP 2p15 / VPS54 2p14

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)VPS54   18652
Cards
Entrez_Gene (NCBI)VPS54  51542  VPS54, GARP complex subunit
AliasesHCC8; PPP1R164; SLP-8p; VPS54L; 
WR; hVps54L
GeneCards (Weizmann)VPS54
Ensembl hg19 (Hinxton)ENSG00000143952 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000143952 [Gene_View]  chr2:63892533-64019080 [Contig_View]  VPS54 [Vega]
ICGC DataPortalENSG00000143952
TCGA cBioPortalVPS54
AceView (NCBI)VPS54
Genatlas (Paris)VPS54
WikiGenes51542
SOURCE (Princeton)VPS54
Genetics Home Reference (NIH)VPS54
Genomic and cartography
GoldenPath hg38 (UCSC)VPS54  -     chr2:63892533-64019080 -  2p15   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VPS54  -     2p15   [Description]    (hg19-Feb_2009)
EnsemblVPS54 - 2p15 [CytoView hg19]  VPS54 - 2p15 [CytoView hg38]
Mapping of homologs : NCBIVPS54 [Mapview hg19]  VPS54 [Mapview hg38]
OMIM614633   
Gene and transcription
Genbank (Entrez)AF102177 AK002205 AK025545 AK094019 AK124436
RefSeq transcript (Entrez)NM_001005739 NM_016516
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VPS54
Cluster EST : UnigeneHs.48499 [ NCBI ]
CGAP (NCI)Hs.48499
Alternative Splicing GalleryENSG00000143952
Gene ExpressionVPS54 [ NCBI-GEO ]   VPS54 [ EBI - ARRAY_EXPRESS ]   VPS54 [ SEEK ]   VPS54 [ MEM ]
Gene Expression Viewer (FireBrowse)VPS54 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)51542
GTEX Portal (Tissue expression)VPS54
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9P1Q0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9P1Q0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9P1Q0
Splice isoforms : SwissVarQ9P1Q0
PhosPhoSitePlusQ9P1Q0
Domains : Interpro (EBI)Vps54_C    VPS54_N   
Domain families : Pfam (Sanger)Vps54 (PF07928)    Vps54_N (PF10475)   
Domain families : Pfam (NCBI)pfam07928    pfam10475   
Conserved Domain (NCBI)VPS54
DMDM Disease mutations51542
Blocks (Seattle)VPS54
SuperfamilyQ9P1Q0
Human Protein AtlasENSG00000143952
Peptide AtlasQ9P1Q0
HPRD10302
IPIIPI00480073   IPI00555953   IPI00555893   IPI00163718   IPI00556232   IPI00952842   
Protein Interaction databases
DIP (DOE-UCLA)Q9P1Q0
IntAct (EBI)Q9P1Q0
FunCoupENSG00000143952
BioGRIDVPS54
STRING (EMBL)VPS54
ZODIACVPS54
Ontologies - Pathways
QuickGOQ9P1Q0
Ontology : AmiGOGARP complex  protein binding  nucleoplasm  Golgi apparatus  trans-Golgi network  cytosol  Golgi to vacuole transport  lysosomal transport  protein transport  syntaxin binding  trans-Golgi network membrane  growth  retrograde transport, endosome to Golgi  perinuclear region of cytoplasm  homeostasis of number of cells within a tissue  musculoskeletal movement  neurofilament cytoskeleton organization  
Ontology : EGO-EBIGARP complex  protein binding  nucleoplasm  Golgi apparatus  trans-Golgi network  cytosol  Golgi to vacuole transport  lysosomal transport  protein transport  syntaxin binding  trans-Golgi network membrane  growth  retrograde transport, endosome to Golgi  perinuclear region of cytoplasm  homeostasis of number of cells within a tissue  musculoskeletal movement  neurofilament cytoskeleton organization  
NDEx NetworkVPS54
Atlas of Cancer Signalling NetworkVPS54
Wikipedia pathwaysVPS54
Orthology - Evolution
OrthoDB51542
GeneTree (enSembl)ENSG00000143952
Phylogenetic Trees/Animal Genes : TreeFamVPS54
HOVERGENQ9P1Q0
HOGENOMQ9P1Q0
Homologs : HomoloGeneVPS54
Homology/Alignments : Family Browser (UCSC)VPS54
Gene fusions - Rearrangements
Fusion: TCGAVPS54 2p14 PELI1 2p14 BLCA
Fusion: TCGAWDPCP 2p15 VPS54 2p14 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVPS54 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VPS54
dbVarVPS54
ClinVarVPS54
1000_GenomesVPS54 
Exome Variant ServerVPS54
ExAC (Exome Aggregation Consortium)VPS54 (select the gene name)
Genetic variants : HAPMAP51542
Genomic Variants (DGV)VPS54 [DGVbeta]
DECIPHERVPS54 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVPS54 
Mutations
ICGC Data PortalVPS54 
TCGA Data PortalVPS54 
Broad Tumor PortalVPS54
OASIS PortalVPS54 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVPS54  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVPS54
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 VPS54
DgiDB (Drug Gene Interaction Database)VPS54
DoCM (Curated mutations)VPS54 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VPS54 (select a term)
intoGenVPS54
Cancer3DVPS54(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM614633   
Orphanet
MedgenVPS54
Genetic Testing Registry VPS54
NextProtQ9P1Q0 [Medical]
TSGene51542
GENETestsVPS54
Target ValidationVPS54
Huge Navigator VPS54 [HugePedia]
snp3D : Map Gene to Disease51542
BioCentury BCIQVPS54
ClinGenVPS54
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD51542
Chemical/Pharm GKB GenePA134920394
Clinical trialVPS54
Miscellaneous
canSAR (ICR)VPS54 (select the gene name)
Probes
Litterature
PubMed19 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVPS54
EVEXVPS54
GoPubMedVPS54
iHOPVPS54
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Jun 7 13:02:36 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.