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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret jlhuret@AtlasGeneticsOncology.org
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ASPSCR1 (Alveolar soft part sarcoma critical region 1)

Identity

Other namesASPL (Alveolar soft part sarcoma locus)
HGNC (Hugo) ASPSCR1
LocusID (NCBI) 79058
Location 17q25.3
Location_base_pair Starts at 79935426 and ends at 79975282 bp from pter ( according to hg19-Feb_2009)  [Mapping]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics

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

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
  

Other Solid tumors implicated (Data extracted from papers in the Atlas)

Solid Tumors AmeloblastomID5945 MedulloblastomaID5065 rhabID5004

External links

Nomenclature
HGNC (Hugo)ASPSCR1   13825
Cards
AtlasASPSCR1ID358
Entrez_Gene (NCBI)ASPSCR1  79058  alveolar soft part sarcoma chromosome region, candidate 1
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
cBioPortalASPSCR1
AceView (NCBI)ASPSCR1
Genatlas (Paris)ASPSCR1
WikiGenes79058
SOURCE (Princeton)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 : Fast-db (Paris)GSHG0012911
Alternative Splicing GalleryENSG00000169696
Gene ExpressionASPSCR1 [ NCBI-GEO ]     ASPSCR1 [ SEEK ]   ASPSCR1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BZE9 (Uniprot)
NextProtQ9BZE9  [Medical]
With graphics : InterProQ9BZE9
Splice isoforms : SwissVarQ9BZE9 (Swissvar)
Domaine pattern : Prosite (Expaxy)UBX (PS50033)   
Domains : Interpro (EBI)TUG/UBX4    Ubiquitin-rel_dom    UBX_dom   
Related proteins : CluSTrQ9BZE9
Domain families : Pfam (Sanger)TUG-UBL1 (PF11470)    UBX (PF00789)   
Domain families : Pfam (NCBI)pfam11470    pfam00789   
Domain families : Smart (EMBL)UBX (SM00166)  
DMDM Disease mutations79058
Blocks (Seattle)Q9BZE9
Human Protein AtlasENSG00000169696
Peptide AtlasQ9BZE9
HPRD06947
IPIIPI00332071   IPI00065276   IPI00787285   IPI00385430   
Protein Interaction databases
DIP (DOE-UCLA)Q9BZE9
IntAct (EBI)Q9BZE9
FunCoupENSG00000169696
BioGRIDASPSCR1
IntegromeDBASPSCR1
STRING (EMBL)ASPSCR1
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  membrane organization  
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  membrane organization  
Pathways : KEGGTranscriptional misregulation in cancer   
REACTOMEQ9BZE9 [protein]
REACTOME PathwaysREACT_11123 Membrane Trafficking [pathway]
Protein Interaction DatabaseASPSCR1
DoCM (Curated mutations)ASPSCR1
Wikipedia pathwaysASPSCR1
Gene fusion - rearrangements
Rearrangement : COSMICTFE3 [Xp11.23]  -  ASPSCR1 [17q25.3]
Rearrangement : TICdbASPSCR1 [17q25.3]  -  TFE3 [10q11.21]
Polymorphisms : SNP, variants
NCBI Variation ViewerASPSCR1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ASPSCR1
dbVarASPSCR1
ClinVarASPSCR1
1000_GenomesASPSCR1 
Exome Variant ServerASPSCR1
SNP (GeneSNP Utah)ASPSCR1
SNP : HGBaseASPSCR1
Genetic variants : HAPMAPASPSCR1
Genomic Variants (DGV)ASPSCR1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000169696 
Cancer Gene: CensusASPSCR1 
Somatic Mutations in Cancer : COSMICASPSCR1 
CONAN: Copy Number AnalysisASPSCR1 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:79935426-79975282
Mutations and Diseases : HGMDASPSCR1
OMIM606236    606243   
MedgenASPSCR1
NextProtQ9BZE9 [Medical]
GENETestsASPSCR1
Disease Genetic AssociationASPSCR1
Huge Navigator ASPSCR1 [HugePedia]  ASPSCR1 [HugeCancerGEM]
snp3D : Map Gene to Disease79058
DGIdb (Drug Gene Interaction db)ASPSCR1
General knowledge
Homologs : HomoloGeneASPSCR1
Homology/Alignments : Family Browser (UCSC)ASPSCR1
Phylogenetic Trees/Animal Genes : TreeFamASPSCR1
Chemical/Protein Interactions : CTD79058
Chemical/Pharm GKB GenePA25058
Clinical trialASPSCR1
Cancer Resource (Charite)ENSG00000169696
Other databases
Probes
ProbeCancer Cytogenetics (Bari)
Litterature
PubMed35 Pubmed reference(s) in Entrez
CoreMineASPSCR1
GoPubMedASPSCR1
iHOPASPSCR1

Bibliography

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
 
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
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written08-2001Jean-Loup Huret

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 ]
URL : http://AtlasGeneticsOncology.org/Genes/ASPSCR1ID358.html

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indexed on : Sat Mar 28 12:41:57 CET 2015

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