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ASPSCR1 (Alveolar soft part sarcoma critical region 1)

Written2001-08Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesalveolar soft part sarcoma chromosome region
Alias_symbol (synonym)ASPS
ASPL
UBXD9
UBXN9
TUG
HGNC (Hugo) ASPSCR1
LocusID (NCBI) 79058
Atlas_Id 358
Location 17q25.3  [Link to chromosome band 17q25]
Location_base_pair Starts at 79935426 and ends at 79975282 bp from pter ( according to hg19-Feb_2009)  [Mapping ASPSCR1.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)
ASPSCR1 (17q25.3) / COL5A3 (19p13.2)ASPSCR1 (17q25.3) / TFE3 (Xp11.23)TBCD (17q25.3) / ASPSCR1 (17q25.3)
TFE3 (Xp11.23) / ASPSCR1 (17q25.3)

DNA/RNA

Description 1872 bp cDNA
Transcription alternative splicing of 47 bp from exon 2 in the 5' untranslated region

Protein

Description 476 amino acids; contains an UBX domain, which may be related to the ubiquitylation pathway
Expression widely expressed in the adult; low expression in fetal tissues

Implicated in

Note
Entity Alveolar soft part sarcoma with ASPSCR1 -TFE3 fusion
Cytogenetics der(X)t(X;17)(p11;q25) is consistently involved; it implicates: 1- the formation of a hybrid gene at the breakpoint, and also, 2- gain in Xp11-pter sequences, and loss of heterozygocity in 11q25-qter, with possible implications
Hybrid/Mutated Gene 5' ASPSCR1-3' TFE3; the reciprocal 5' TFE3 - 3' ASPSCR1 is most often absent. ASPSCR1 is fused in frame to TFE3 exon 3 or 4
Abnormal Protein NH2 term ASPSCR1, fused to the C term of TFE3
Oncogenesis might combine the effect of a fusion protein to that of gene(s) dosage
  
Entity primary renal ASPSCR1-TFE3 tumour
Disease a subset of renal cell carcinoma, which presents with a combination of alveolar soft part sarcoma-like features and epithelial features is found to carry this anomaly
Cytogenetics balanced t(X;17)(p11.2;q25), in contrast with what is found in the alveolar soft part sarcoma (see above)
Hybrid/Mutated Gene 5' ASPSCR1-3' TFE3
Abnormal Protein NH2 term ASPSCR1, fused to the C term of TFE3
  

Bibliography

Primary renal neoplasms with the ASPL-TFE3 gene fusion of alveolar soft part sarcoma: a distinctive tumor entity previously included among renal cell carcinomas of children and adolescents.
Argani P, Antonescu CR, Illei PB, Lui MY, Timmons CF, Newbury R, Reuter VE, Garvin AJ, Perez-Atayde AR, Fletcher JA, Beckwith JB, Bridge JA, Ladanyi M
The American journal of pathology. 2001 ; 159 (1) : 179-192.
PMID 11438465
 
The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25.
Ladanyi M, Lui MY, Antonescu CR, Krause-Boehm A, Meindl A, Argani P, Healey JH, Ueda T, Yoshikawa H, Meloni-Ehrig A, Sorensen PH, Mertens F, Mandahl N, van den Berghe H, Sciot R, Cin PD, Bridge J
Oncogene. 2001 ; 20 (1) : 48-57.
PMID 11244503
 

Citation

This paper should be referenced as such :
Huret, JL
ASPSCR1 (alveolar soft part sarcoma critical region 1)
Atlas Genet Cytogenet Oncol Haematol. 2001;5(4):252-253.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ASPSCR1ID358.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 4 ]
  Soft Tissues: Alveolar soft part sarcoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Kidney: Renal cell carcinomas with MiT family translocation
Kidney: Renal cell carcinoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Soft tissue tumors: an overview


External links

Nomenclature
HGNC (Hugo)ASPSCR1   13825
Cards
AtlasASPSCR1ID358
Entrez_Gene (NCBI)ASPSCR1  79058  alveolar soft part sarcoma chromosome region, candidate 1
AliasesASPCR1; ASPL; ASPS; RCC17; 
TUG; UBXD9; UBXN9
GeneCards (Weizmann)ASPSCR1
Ensembl hg19 (Hinxton)ENSG00000169696 [Gene_View]  chr17:79935426-79975282 [Contig_View]  ASPSCR1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000169696 [Gene_View]  chr17:79935426-79975282 [Contig_View]  ASPSCR1 [Vega]
ICGC DataPortalENSG00000169696
TCGA cBioPortalASPSCR1
AceView (NCBI)ASPSCR1
Genatlas (Paris)ASPSCR1
WikiGenes79058
SOURCE (Princeton)ASPSCR1
Genetics Home Reference (NIH)ASPSCR1
Genomic and cartography
GoldenPath hg19 (UCSC)ASPSCR1  -     chr17:79935426-79975282 +  17q25   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ASPSCR1  -     17q25   [Description]    (hg38-Dec_2013)
EnsemblASPSCR1 - 17q25 [CytoView hg19]  ASPSCR1 - 17q25 [CytoView hg38]
Mapping of homologs : NCBIASPSCR1 [Mapview hg19]  ASPSCR1 [Mapview hg38]
OMIM606236   606243   
Gene and transcription
Genbank (Entrez)AF324219 AK057403 AK057851 AK090682 AK126967
RefSeq transcript (Entrez)NM_001251888 NM_024083
RefSeq genomic (Entrez)NC_000017 NC_018928 NG_030375 NT_010663 NW_004929408
Consensus coding sequences : CCDS (NCBI)ASPSCR1
Cluster EST : UnigeneHs.298351 [ NCBI ]
CGAP (NCI)Hs.298351
Alternative Splicing GalleryENSG00000169696
Gene ExpressionASPSCR1 [ NCBI-GEO ]   ASPSCR1 [ EBI - ARRAY_EXPRESS ]   ASPSCR1 [ SEEK ]   ASPSCR1 [ MEM ]
Gene Expression Viewer (FireBrowse)ASPSCR1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)79058
GTEX Portal (Tissue expression)ASPSCR1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BZE9   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BZE9  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BZE9
Splice isoforms : SwissVarQ9BZE9
PhosPhoSitePlusQ9BZE9
Domaine pattern : Prosite (Expaxy)UBX (PS50033)   
Domains : Interpro (EBI)TUG-UBL1    Ubiquitin-rel_dom    UBX_dom   
Domain families : Pfam (Sanger)TUG-UBL1 (PF11470)    UBX (PF00789)   
Domain families : Pfam (NCBI)pfam11470    pfam00789   
Domain families : Smart (EMBL)UBX (SM00166)  
Conserved Domain (NCBI)ASPSCR1
DMDM Disease mutations79058
Blocks (Seattle)ASPSCR1
SuperfamilyQ9BZE9
Human Protein AtlasENSG00000169696
Peptide AtlasQ9BZE9
HPRD06947
IPIIPI00332071   IPI00065276   IPI00787285   IPI00385430   
Protein Interaction databases
DIP (DOE-UCLA)Q9BZE9
IntAct (EBI)Q9BZE9
FunCoupENSG00000169696
BioGRIDASPSCR1
STRING (EMBL)ASPSCR1
ZODIACASPSCR1
Ontologies - Pathways
QuickGOQ9BZE9
Ontology : AmiGOmolecular_function  protein binding  cellular_component  nucleoplasm  cytosol  plasma membrane  intracellular protein transport  biological_process  cytoplasmic side of plasma membrane  endomembrane system  vesicle membrane  extrinsic component of membrane  endoplasmic reticulum-Golgi intermediate compartment membrane  glucose homeostasis  intracellular membrane-bounded organelle  regulation of glucose import  perinuclear region of cytoplasm  
Ontology : EGO-EBImolecular_function  protein binding  cellular_component  nucleoplasm  cytosol  plasma membrane  intracellular protein transport  biological_process  cytoplasmic side of plasma membrane  endomembrane system  vesicle membrane  extrinsic component of membrane  endoplasmic reticulum-Golgi intermediate compartment membrane  glucose homeostasis  intracellular membrane-bounded organelle  regulation of glucose import  perinuclear region of cytoplasm  
Pathways : KEGGTranscriptional misregulation in cancer   
REACTOMEQ9BZE9 [protein]
REACTOME PathwaysR-HSA-1445148 Translocation of GLUT4 to the plasma membrane [pathway]
NDEx NetworkASPSCR1
Atlas of Cancer Signalling NetworkASPSCR1
Wikipedia pathwaysASPSCR1
Orthology - Evolution
OrthoDB79058
GeneTree (enSembl)ENSG00000169696
Phylogenetic Trees/Animal Genes : TreeFamASPSCR1
HOVERGENQ9BZE9
HOGENOMQ9BZE9
Homologs : HomoloGeneASPSCR1
Homology/Alignments : Family Browser (UCSC)ASPSCR1
Gene fusions - Rearrangements
Fusion : MitelmanASPSCR1/COL5A3 [17q25.3/19p13.2]  
Fusion : MitelmanASPSCR1/TFE3 [17q25.3/Xp11.23]  [t(X;17)(p11;q25)]  
Fusion : MitelmanTBCD/ASPSCR1 [17q25.3/17q25.3]  [t(17;17)(q25;q25)]  
Fusion : COSMICASPSCR1 [17q25.3]  -  TFE3 [Xp11.23]  [fusion_393]  [fusion_394]  [fusion_395]  [fusion_396]  [fusion_814]  
Fusion : COSMICTFE3 [Xp11.23]  -  ASPSCR1 [17q25.3]  [fusion_769]  [fusion_782]  [fusion_797]  [fusion_798]  [fusion_838]  [fusion_875]  
Fusion: TCGAASPSCR1 17q25.3 COL5A3 19p13.2 BRCA
Fusion: TCGATBCD 17q25.3 ASPSCR1 17q25.3 LUSC
Fusion : TICdbASPSCR1 [17q25.3]  -  TFE3 [Xp11.23]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerASPSCR1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ASPSCR1
dbVarASPSCR1
ClinVarASPSCR1
1000_GenomesASPSCR1 
Exome Variant ServerASPSCR1
ExAC (Exome Aggregation Consortium)ASPSCR1 (select the gene name)
Genetic variants : HAPMAP79058
Genomic Variants (DGV)ASPSCR1 [DGVbeta]
DECIPHER (Syndromes)17:79935426-79975282  ENSG00000169696
CONAN: Copy Number AnalysisASPSCR1 
Mutations
ICGC Data PortalASPSCR1 
TCGA Data PortalASPSCR1 
Broad Tumor PortalASPSCR1
OASIS PortalASPSCR1 [ Somatic mutations - Copy number]
Cancer Gene: CensusASPSCR1 
Somatic Mutations in Cancer : COSMICASPSCR1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDASPSCR1
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 ASPSCR1
DgiDB (Drug Gene Interaction Database)ASPSCR1
DoCM (Curated mutations)ASPSCR1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ASPSCR1 (select a term)
intoGenASPSCR1
NCG5 (London)ASPSCR1
Cancer3DASPSCR1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606236    606243   
Orphanet17527    21643   
MedgenASPSCR1
Genetic Testing Registry ASPSCR1
NextProtQ9BZE9 [Medical]
TSGene79058
GENETestsASPSCR1
Huge Navigator ASPSCR1 [HugePedia]
snp3D : Map Gene to Disease79058
BioCentury BCIQASPSCR1
ClinGenASPSCR1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD79058
Chemical/Pharm GKB GenePA25058
Clinical trialASPSCR1
Miscellaneous
canSAR (ICR)ASPSCR1 (select the gene name)
Probes
Litterature
PubMed40 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineASPSCR1
EVEXASPSCR1
GoPubMedASPSCR1
iHOPASPSCR1
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 Nov 18 20:07:13 CET 2016

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jlhuret@AtlasGeneticsOncology.org.