Atlas of Genetics and Cytogenetics in Oncology and Haematology

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VPS4B (vacuolar protein sorting 4 homolog B)

Identity

Alias_namesSKD1
suppressor of K transport defect 1
vacuolar protein sorting 4B (yeast)
vacuolar protein sorting 4 homolog B (S. cerevisiae)
Alias_symbol (synonym)VPS4-2
SKD1B
Other aliasMIG1
HGNC (Hugo) VPS4B
LocusID (NCBI) 9525
Atlas_Id 52680
Location 18q21.33  [Link to chromosome band 18q21]
Location_base_pair Starts at 63389192 and ends at 63422519 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BCL2 (18q21.33) / VPS4B (18q21.33)VPS4B (18q21.33) / ATP6V1A (3q13.2)VPS4B (18q21.33) / SLC22A15 (1p13.1)
VPS4B 18q21.33 / SLC22A15 1p13.1

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(1;18)(p13;q21) VPS4B/SLC22A15

External links

Nomenclature
HGNC (Hugo)VPS4B   10895
Cards
Entrez_Gene (NCBI)VPS4B  9525  vacuolar protein sorting 4 homolog B
AliasesMIG1; SKD1; SKD1B; VPS4-2
GeneCards (Weizmann)VPS4B
Ensembl hg19 (Hinxton)ENSG00000119541 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000119541 [Gene_View]  ENSG00000119541 [Sequence]  chr18:63389192-63422519 [Contig_View]  VPS4B [Vega]
ICGC DataPortalENSG00000119541
TCGA cBioPortalVPS4B
AceView (NCBI)VPS4B
Genatlas (Paris)VPS4B
WikiGenes9525
SOURCE (Princeton)VPS4B
Genetics Home Reference (NIH)VPS4B
Genomic and cartography
GoldenPath hg38 (UCSC)VPS4B  -     chr18:63389192-63422519 -  18q21.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VPS4B  -     18q21.33   [Description]    (hg19-Feb_2009)
EnsemblVPS4B - 18q21.33 [CytoView hg19]  VPS4B - 18q21.33 [CytoView hg38]
Mapping of homologs : NCBIVPS4B [Mapview hg19]  VPS4B [Mapview hg38]
OMIM609983   
Gene and transcription
Genbank (Entrez)AF038960 AF195514 AK290932 AK291253 AK308892
RefSeq transcript (Entrez)NM_004869
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VPS4B
Cluster EST : UnigeneHs.126550 [ NCBI ]
CGAP (NCI)Hs.126550
Alternative Splicing GalleryENSG00000119541
Gene ExpressionVPS4B [ NCBI-GEO ]   VPS4B [ EBI - ARRAY_EXPRESS ]   VPS4B [ SEEK ]   VPS4B [ MEM ]
Gene Expression Viewer (FireBrowse)VPS4B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9525
GTEX Portal (Tissue expression)VPS4B
Human Protein AtlasENSG00000119541-VPS4B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75351   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75351  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75351
Splice isoforms : SwissVarO75351
Catalytic activity : Enzyme3.6.4.6 [ Enzyme-Expasy ]   3.6.4.63.6.4.6 [ IntEnz-EBI ]   3.6.4.6 [ BRENDA ]   3.6.4.6 [ KEGG ]   
PhosPhoSitePlusO75351
Domaine pattern : Prosite (Expaxy)AAA (PS00674)   
Domains : Interpro (EBI)AAA+_ATPase    ATPase_AAA_core    ATPase_AAA_CS    MIT    P-loop_NTPase    Vps4_C   
Domain families : Pfam (Sanger)AAA (PF00004)    MIT (PF04212)    Vps4_C (PF09336)   
Domain families : Pfam (NCBI)pfam00004    pfam04212    pfam09336   
Domain families : Smart (EMBL)AAA (SM00382)  MIT (SM00745)  
Conserved Domain (NCBI)VPS4B
DMDM Disease mutations9525
Blocks (Seattle)VPS4B
PDB (SRS)1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
PDB (PDBSum)1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
PDB (IMB)1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
PDB (RSDB)1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
Structural Biology KnowledgeBase1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
SCOP (Structural Classification of Proteins)1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
CATH (Classification of proteins structures)1WR0    1XWI    2CPT    2JQH    2JQK    4U7Y   
SuperfamilyO75351
Human Protein Atlas [tissue]ENSG00000119541-VPS4B [tissue]
Peptide AtlasO75351
HPRD15653
IPIIPI00182728   
Protein Interaction databases
DIP (DOE-UCLA)O75351
IntAct (EBI)O75351
FunCoupENSG00000119541
BioGRIDVPS4B
STRING (EMBL)VPS4B
ZODIACVPS4B
Ontologies - Pathways
QuickGOO75351
Ontology : AmiGOcell separation after cytokinesis  spindle pole  protein binding  ATP binding  nucleus  cytoplasm  endosome  centrosome  cytosol  potassium ion transport  nucleus organization  mitotic metaphase plate congression  protein C-terminus binding  endosome membrane  regulation of centrosome duplication  positive regulation of G2/M transition of mitotic cell cycle  protein transport  endosomal transport  endosomal transport  macroautophagy  ATPase activity  viral life cycle  viral release from host cell  cholesterol transport  late endosome membrane  endosome to lysosome transport via multivesicular body sorting pathway  response to lipid  multivesicular body assembly  viral budding via host ESCRT complex  ATPase activity, coupled  ATPase activity, coupled  identical protein binding  protein homodimerization activity  ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway  positive regulation of viral process  regulation of viral process  protein depolymerization  negative regulation of cell death  late endosomal microautophagy  extracellular exosome  Flemming body  ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway  regulation of mitotic spindle assembly  positive regulation of viral release from host cell  negative regulation of exosomal secretion  positive regulation of exosomal secretion  positive regulation of centriole elongation  positive regulation of viral life cycle  ESCRT III complex disassembly  
Ontology : EGO-EBIcell separation after cytokinesis  spindle pole  protein binding  ATP binding  nucleus  cytoplasm  endosome  centrosome  cytosol  potassium ion transport  nucleus organization  mitotic metaphase plate congression  protein C-terminus binding  endosome membrane  regulation of centrosome duplication  positive regulation of G2/M transition of mitotic cell cycle  protein transport  endosomal transport  endosomal transport  macroautophagy  ATPase activity  viral life cycle  viral release from host cell  cholesterol transport  late endosome membrane  endosome to lysosome transport via multivesicular body sorting pathway  response to lipid  multivesicular body assembly  viral budding via host ESCRT complex  ATPase activity, coupled  ATPase activity, coupled  identical protein binding  protein homodimerization activity  ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway  positive regulation of viral process  regulation of viral process  protein depolymerization  negative regulation of cell death  late endosomal microautophagy  extracellular exosome  Flemming body  ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway  regulation of mitotic spindle assembly  positive regulation of viral release from host cell  negative regulation of exosomal secretion  positive regulation of exosomal secretion  positive regulation of centriole elongation  positive regulation of viral life cycle  ESCRT III complex disassembly  
NDEx NetworkVPS4B
Atlas of Cancer Signalling NetworkVPS4B
Wikipedia pathwaysVPS4B
Orthology - Evolution
OrthoDB9525
GeneTree (enSembl)ENSG00000119541
Phylogenetic Trees/Animal Genes : TreeFamVPS4B
HOVERGENO75351
HOGENOMO75351
Homologs : HomoloGeneVPS4B
Homology/Alignments : Family Browser (UCSC)VPS4B
Gene fusions - Rearrangements
Fusion : MitelmanVPS4B/SLC22A15 [18q21.33/1p13.1]  
Fusion PortalVPS4B 18q21.33 SLC22A15 1p13.1 LUAD
Fusion : QuiverVPS4B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVPS4B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VPS4B
dbVarVPS4B
ClinVarVPS4B
1000_GenomesVPS4B 
Exome Variant ServerVPS4B
ExAC (Exome Aggregation Consortium)ENSG00000119541
GNOMAD BrowserENSG00000119541
Genetic variants : HAPMAP9525
Genomic Variants (DGV)VPS4B [DGVbeta]
DECIPHERVPS4B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVPS4B 
Mutations
ICGC Data PortalVPS4B 
TCGA Data PortalVPS4B 
Broad Tumor PortalVPS4B
OASIS PortalVPS4B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVPS4B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVPS4B
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 VPS4B
DgiDB (Drug Gene Interaction Database)VPS4B
DoCM (Curated mutations)VPS4B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VPS4B (select a term)
intoGenVPS4B
Cancer3DVPS4B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609983   
Orphanet
DisGeNETVPS4B
MedgenVPS4B
Genetic Testing Registry VPS4B
NextProtO75351 [Medical]
TSGene9525
GENETestsVPS4B
Target ValidationVPS4B
Huge Navigator VPS4B [HugePedia]
snp3D : Map Gene to Disease9525
BioCentury BCIQVPS4B
ClinGenVPS4B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9525
Chemical/Pharm GKB GenePA35795
Clinical trialVPS4B
Miscellaneous
canSAR (ICR)VPS4B (select the gene name)
Probes
Litterature
PubMed73 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVPS4B
EVEXVPS4B
GoPubMedVPS4B
iHOPVPS4B
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Jun 22 16:57:16 CEST 2018
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