Atlas of Genetics and Cytogenetics in Oncology and Haematology

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VPS72 (vacuolar protein sorting 72 homolog)

Identity

Alias (NCBI)CFL1
Swc2
TCFL1
YL-1
YL1
HGNC (Hugo) VPS72
HGNC Alias symbYL-1
YL1
Swc2
HGNC Previous nameTCFL1
HGNC Previous nametranscription factor-like 1
 vacuolar protein sorting 72 (yeast)
 vacuolar protein sorting 72 homolog (S. cerevisiae)
LocusID (NCBI) 6944
Atlas_Id 42497
Location 1q21.3  [Link to chromosome band 1q21]
Location_base_pair Starts at 151176306 and ends at 151190197 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)
TMEM184B (22q13.1) / VPS72 (1q21.3)UBE2Q1 (1q21.3) / VPS72 (1q21.3)VPS72 (1q21.3) / MUC4 (3q29)
VPS72 (1q21.3) / PNN (14q21.1)VPS72 (1q21.3) / ROBO2 (3p12.3)VPS72 (1q21.3) / RORC (1q21.3)
VPS72 (1q21.3) / TGM3 (20p13)VPS72 (1q21.3) / TMOD4 (1q21.3)VPS72 (1q21.3) / VPS72 (1q21.3)
VPS72 1q21.3 / ROBO2 3p12.3VPS72 1q21.3 / RORC 1q21.3

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) [ 2 ]
  VPS72/RORC (1q21)
t(1;3)(q21;p12) VPS72/ROBO2

External links

Nomenclature
HGNC (Hugo)VPS72   11644
Cards
Entrez_Gene (NCBI)VPS72    vacuolar protein sorting 72 homolog
AliasesCFL1; Swc2; TCFL1; YL-1; 
YL1
GeneCards (Weizmann)VPS72
Ensembl hg19 (Hinxton)ENSG00000163159 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000163159 [Gene_View]  ENSG00000163159 [Sequence]  chr1:151176306-151190197 [Contig_View]  VPS72 [Vega]
ICGC DataPortalENSG00000163159
TCGA cBioPortalVPS72
AceView (NCBI)VPS72
Genatlas (Paris)VPS72
SOURCE (Princeton)VPS72
Genetics Home Reference (NIH)VPS72
Genomic and cartography
GoldenPath hg38 (UCSC)VPS72  -     chr1:151176306-151190197 -  1q21.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VPS72  -     1q21.3   [Description]    (hg19-Feb_2009)
GoldenPathVPS72 - 1q21.3 [CytoView hg19]  VPS72 - 1q21.3 [CytoView hg38]
ImmunoBaseENSG00000163159
genome Data Viewer NCBIVPS72 [Mapview hg19]  
OMIM600607   
Gene and transcription
Genbank (Entrez)AA128103 AK222935 AK222939 AK225130 AK297565
RefSeq transcript (Entrez)NM_001271087 NM_001271088 NM_005997
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VPS72
Alternative Splicing GalleryENSG00000163159
Gene ExpressionVPS72 [ NCBI-GEO ]   VPS72 [ EBI - ARRAY_EXPRESS ]   VPS72 [ SEEK ]   VPS72 [ MEM ]
Gene Expression Viewer (FireBrowse)VPS72 [ Firebrowse - Broad ]
GenevisibleExpression of VPS72 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6944
GTEX Portal (Tissue expression)VPS72
Human Protein AtlasENSG00000163159-VPS72 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15906   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ15906  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ15906
Splice isoforms : SwissVarQ15906
PhosPhoSitePlusQ15906
Domains : Interpro (EBI)Vps72/YL1    Vps72/YL1_C   
Domain families : Pfam (Sanger)YL1 (PF05764)    YL1_C (PF08265)   
Domain families : Pfam (NCBI)pfam05764    pfam08265   
Domain families : Smart (EMBL)YL1_C (SM00993)  
Conserved Domain (NCBI)VPS72
Blocks (Seattle)VPS72
PDB (RSDB)5FUG   
PDB Europe5FUG   
PDB (PDBSum)5FUG   
PDB (IMB)5FUG   
Structural Biology KnowledgeBase5FUG   
SCOP (Structural Classification of Proteins)5FUG   
CATH (Classification of proteins structures)5FUG   
SuperfamilyQ15906
Human Protein Atlas [tissue]ENSG00000163159-VPS72 [tissue]
Peptide AtlasQ15906
HPRD02791
IPIIPI00020434   IPI00844510   
Protein Interaction databases
DIP (DOE-UCLA)Q15906
IntAct (EBI)Q15906
BioGRIDVPS72
STRING (EMBL)VPS72
ZODIACVPS72
Ontologies - Pathways
QuickGOQ15906
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  DNA binding  protein binding  nucleus  nucleoplasm  nuclear speck  protein-containing complex  somatic stem cell population maintenance  histone binding  histone exchange  histone exchange  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  DNA binding  protein binding  nucleus  nucleoplasm  nuclear speck  protein-containing complex  somatic stem cell population maintenance  histone binding  histone exchange  histone exchange  
NDEx NetworkVPS72
Atlas of Cancer Signalling NetworkVPS72
Wikipedia pathwaysVPS72
Orthology - Evolution
OrthoDB6944
GeneTree (enSembl)ENSG00000163159
Phylogenetic Trees/Animal Genes : TreeFamVPS72
HOGENOMQ15906
Homologs : HomoloGeneVPS72
Homology/Alignments : Family Browser (UCSC)VPS72
Gene fusions - Rearrangements
Fusion : MitelmanVPS72/ROBO2 [1q21.3/3p12.3]  
Fusion : MitelmanVPS72/RORC [1q21.3/1q21.3]  
Fusion PortalVPS72 1q21.3 ROBO2 3p12.3 LUAD
Fusion PortalVPS72 1q21.3 RORC 1q21.3 LUAD
Fusion : QuiverVPS72
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVPS72 [hg38]
dbVarVPS72
ClinVarVPS72
MonarchVPS72
1000_GenomesVPS72 
Exome Variant ServerVPS72
GNOMAD BrowserENSG00000163159
Varsome BrowserVPS72
Genomic Variants (DGV)VPS72 [DGVbeta]
DECIPHERVPS72 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVPS72 
Mutations
ICGC Data PortalVPS72 
TCGA Data PortalVPS72 
Broad Tumor PortalVPS72
OASIS PortalVPS72 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVPS72  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DVPS72
Mutations and Diseases : HGMDVPS72
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch VPS72
DgiDB (Drug Gene Interaction Database)VPS72
DoCM (Curated mutations)VPS72 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VPS72 (select a term)
intoGenVPS72
Cancer3DVPS72(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600607   
Orphanet
DisGeNETVPS72
MedgenVPS72
Genetic Testing Registry VPS72
NextProtQ15906 [Medical]
GENETestsVPS72
Target ValidationVPS72
Huge Navigator VPS72 [HugePedia]
ClinGenVPS72
Clinical trials, drugs, therapy
MyCancerGenomeVPS72
Protein Interactions : CTD
Pharm GKB GenePA36396
PharosQ15906
Clinical trialVPS72
Miscellaneous
canSAR (ICR)VPS72 (select the gene name)
HarmonizomeVPS72
DataMed IndexVPS72
Probes
Litterature
PubMed39 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXVPS72
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 1 18:44:10 CET 2021
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