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VPS35 (VPS35 retromer complex component)

Identity

Other namesMEM3
PARK17
HGNC (Hugo) VPS35
LocusID (NCBI) 55737
Atlas_Id 52597
Location 16q11.2
Location_base_pair Starts at 46693589 and ends at 46723144 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
CD63 (12q13.2) / VPS35 (16q11.2)ORC6 (16q11.2) / VPS35 (16q11.2)PUM2 (2p24.1) / VPS35 (16q11.2)
VPS35 (16q11.2) / DCN (12q21.33)VPS35 (16q11.2) / MYLK3 (16q11.2)VPS35 (16q11.2) / PHKB (16q12.1)
VPS35 (16q11.2) / SLC6A2 (16q12.2)VPS35 (16q11.2) / VPS35 (16q11.2)WAC (10p12.1) / VPS35 (16q11.2)
ORC6 16q11.2 / VPS35 16q11.2VPS35 16q11.2 / PHKB 16q12.1VPS35 16q11.2 / SLC6A2 16q12.2

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)VPS35   13487
Cards
Entrez_Gene (NCBI)VPS35  55737  VPS35 retromer complex component
AliasesMEM3; PARK17
GeneCards (Weizmann)VPS35
Ensembl hg19 (Hinxton)ENSG00000069329 [Gene_View]  chr16:46693589-46723144 [Contig_View]  VPS35 [Vega]
Ensembl hg38 (Hinxton)ENSG00000069329 [Gene_View]  chr16:46693589-46723144 [Contig_View]  VPS35 [Vega]
ICGC DataPortalENSG00000069329
TCGA cBioPortalVPS35
AceView (NCBI)VPS35
Genatlas (Paris)VPS35
WikiGenes55737
SOURCE (Princeton)VPS35
Genomic and cartography
GoldenPath hg19 (UCSC)VPS35  -     chr16:46693589-46723144 -  16q11.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)VPS35  -     16q11.2   [Description]    (hg38-Dec_2013)
EnsemblVPS35 - 16q11.2 [CytoView hg19]  VPS35 - 16q11.2 [CytoView hg38]
Mapping of homologs : NCBIVPS35 [Mapview hg19]  VPS35 [Mapview hg38]
OMIM601501   614203   
Gene and transcription
Genbank (Entrez)AF086051 AF175265 AF183418 AF186382 AF191298
RefSeq transcript (Entrez)NM_018206
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_029970 NT_010498 NW_004929402
Consensus coding sequences : CCDS (NCBI)VPS35
Cluster EST : UnigeneHs.454528 [ NCBI ]
CGAP (NCI)Hs.454528
Alternative Splicing GalleryENSG00000069329
Gene ExpressionVPS35 [ NCBI-GEO ]   VPS35 [ EBI - ARRAY_EXPRESS ]   VPS35 [ SEEK ]   VPS35 [ MEM ]
Gene Expression Viewer (FireBrowse)VPS35 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55737
GTEX Portal (Tissue expression)VPS35
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96QK1 (Uniprot)
NextProtQ96QK1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96QK1
Splice isoforms : SwissVarQ96QK1 (Swissvar)
PhosPhoSitePlusQ96QK1
Domains : Interpro (EBI)ARM-type_fold    Vps35   
Domain families : Pfam (Sanger)Vps35 (PF03635)   
Domain families : Pfam (NCBI)pfam03635   
DMDM Disease mutations55737
Blocks (Seattle)VPS35
PDB (SRS)2R17   
PDB (PDBSum)2R17   
PDB (IMB)2R17   
PDB (RSDB)2R17   
Structural Biology KnowledgeBase2R17   
SCOP (Structural Classification of Proteins)2R17   
CATH (Classification of proteins structures)2R17   
SuperfamilyQ96QK1
Human Protein AtlasENSG00000069329
Peptide AtlasQ96QK1
HPRD06085
IPIIPI00018931   IPI01010570   
Protein Interaction databases
DIP (DOE-UCLA)Q96QK1
IntAct (EBI)Q96QK1
FunCoupENSG00000069329
BioGRIDVPS35
STRING (EMBL)VPS35
ZODIACVPS35
Ontologies - Pathways
QuickGOQ96QK1
Ontology : AmiGOprotein binding  lysosomal membrane  endosome  early endosome  late endosome  cytosol  cytosol  intracellular protein transport  protein transporter activity  Wnt signaling pathway  Wnt signaling pathway  regulation of macroautophagy  retromer complex  retromer complex  retromer complex  retromer, cargo-selective complex  regulation of protein stability  retrograde transport, endosome to Golgi  retrograde transport, endosome to Golgi  transcytosis  positive regulation of Wnt protein secretion  extracellular exosome  positive regulation of canonical Wnt signaling pathway  tubular endosome  neuronal postsynaptic density  negative regulation of late endosome to lysosome transport  retrograde transport, endosome to plasma membrane  
Ontology : EGO-EBIprotein binding  lysosomal membrane  endosome  early endosome  late endosome  cytosol  cytosol  intracellular protein transport  protein transporter activity  Wnt signaling pathway  Wnt signaling pathway  regulation of macroautophagy  retromer complex  retromer complex  retromer complex  retromer, cargo-selective complex  regulation of protein stability  retrograde transport, endosome to Golgi  retrograde transport, endosome to Golgi  transcytosis  positive regulation of Wnt protein secretion  extracellular exosome  positive regulation of canonical Wnt signaling pathway  tubular endosome  neuronal postsynaptic density  negative regulation of late endosome to lysosome transport  retrograde transport, endosome to plasma membrane  
NDEx Network
Atlas of Cancer Signalling NetworkVPS35
Wikipedia pathwaysVPS35
Orthology - Evolution
OrthoDB55737
GeneTree (enSembl)ENSG00000069329
Phylogenetic Trees/Animal Genes : TreeFamVPS35
Homologs : HomoloGeneVPS35
Homology/Alignments : Family Browser (UCSC)VPS35
Gene fusions - Rearrangements
Fusion: TCGAORC6 16q11.2 VPS35 16q11.2 BRCA
Fusion: TCGAVPS35 16q11.2 PHKB 16q12.1 BLCA
Fusion: TCGAVPS35 16q11.2 SLC6A2 16q12.2 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerVPS35 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VPS35
dbVarVPS35
ClinVarVPS35
1000_GenomesVPS35 
Exome Variant ServerVPS35
ExAC (Exome Aggregation Consortium)VPS35 (select the gene name)
Genetic variants : HAPMAP55737
Genomic Variants (DGV)VPS35 [DGVbeta]
Mutations
ICGC Data PortalVPS35 
TCGA Data PortalVPS35 
Broad Tumor PortalVPS35
OASIS PortalVPS35 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVPS35 
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 VPS35
DgiDB (Drug Gene Interaction Database)VPS35
DoCM (Curated mutations)VPS35 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VPS35 (select a term)
intoGenVPS35
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)16:46693589-46723144  ENSG00000069329
CONAN: Copy Number AnalysisVPS35 
Mutations and Diseases : HGMDVPS35
OMIM601501    614203   
MedgenVPS35
Genetic Testing Registry VPS35
NextProtQ96QK1 [Medical]
TSGene55737
GENETestsVPS35
Huge Navigator VPS35 [HugePedia]
snp3D : Map Gene to Disease55737
BioCentury BCIQVPS35
ClinGenVPS35
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55737
Chemical/Pharm GKB GenePA37783
Clinical trialVPS35
Miscellaneous
canSAR (ICR)VPS35 (select the gene name)
Probes
Litterature
PubMed114 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVPS35
EVEXVPS35
GoPubMedVPS35
iHOPVPS35
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat May 28 11:27:14 CEST 2016

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