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PRCC (papillary renal cell carcinoma)

Written1999-01François Desangles, Jean-Loup Huret
Laboratoire de Biologie, Hopital du Val de Grace, 75230 Paris, France

(Note : for Links provided by Atlas : click)

Identity

Other namesRCCP1 (renal cell carcinoma, papillary, 1)
HGNC (Hugo) PRCC
LocusID (NCBI) 5546
Atlas_Id 69
Location 1q23.1  [Link to chromosome band 1q23]
Location_base_pair Starts at 156737274 and ends at 156770609 bp from pter ( according to hg19-Feb_2009)  [Mapping PRCC.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)		ARHGAP6 (Xp22.2) / PRCC (1q23.1)EFHC1 (6p12.2) / PRCC (1q23.1)MAD2L2 (1p36.22) / PRCC (1q23.1)
PRCC (1q23.1) / HAPLN2 (1q23.1)PRCC (1q23.1) / TFE3 (Xp11.23)PRCC (1q23.1) / TMED5 (1p22.1)
SF3B2 (11q13.1) / PRCC (1q23.1)TFE3 (Xp11.23) / PRCC (1q23.1)YY1AP1 (1q22) / PRCC (1q23.1)

DNA/RNA

Description cDNA of 2039 bp
Transcription 1989 bp RNA; coding sequence: CDS 191...1666

Protein

Description 491 amino acids; 52 kDa; proline/leucine/glycine rich domain of 150 amino acids in N-term
Expression wide; in the fetus and in the adult
Homology none is known

Implicated in

Note
Entity t(X;1)(p11.2;q21.2) in renal cell carcinoma --> PRCC/TFE3
Disease t(X;1) is a very rare subtype of papillary renal cell carcinoma
Prognosis overall 5-yr survival rate around 85%
Hybrid/Mutated Gene 5' PRCC- 3' TFE3; variable breakpoint in PRCC; breakpoint in the 1st intron of TFE3
 
Abnormal Protein N-term PRCC with the proline rich sequence fused to most of TFE3, including the ; the reciprocal TFE3-PRCC is expressed; it is to be noted that the normal TFE3 transcript is lost in female patients.
  

Bibliography

The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene.
Sidhar SK, Clark J, Gill S, Hamoudi R, Crew AJ, Gwilliam R, Ross M, Linehan WM, Birdsall S, Shipley J, Cooper CS
Human molecular genetics. 1996 ; 5 (9) : 1333-1338.
PMID 8872474
 
Fusion of the transcription factor TFE3 gene to a novel gene, PRCC, in t(X;1)(p11;q21)-positive papillary renal cell carcinomas.
Weterman MA, Wilbrink M, Geurts van Kessel A
Proceedings of the National Academy of Sciences of the United States of America. 1996 ; 93 (26) : 15294-15298.
PMID 8986805
 

Citation

This paper should be referenced as such :
Desangles, F ; Huret, JL
PRCC (papillary renal cell carcinoma)
Atlas Genet Cytogenet Oncol Haematol. 1999;3(2):56-56.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PRCCID69.html

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  Kidney: Papillary renal cell carcinoma
Kidney: Renal cell carcinoma: an overview
Kidney: Renal cell carcinoma with t(X;1)(p11;q21) PRCC/TFE3

External links

Nomenclature
HGNC (Hugo)PRCC   9343
Cards
AtlasPRCCID69
Entrez_Gene (NCBI)PRCC  5546  papillary renal cell carcinoma (translocation-associated)
AliasesRCCP1; TPRC
GeneCards (Weizmann)PRCC
Ensembl hg19 (Hinxton)ENSG00000143294 [Gene_View]  chr1:156737274-156770609 [Contig_View]  PRCC [Vega]
Ensembl hg38 (Hinxton)ENSG00000143294 [Gene_View]  chr1:156737274-156770609 [Contig_View]  PRCC [Vega]
ICGC DataPortalENSG00000143294
TCGA cBioPortalPRCC
AceView (NCBI)PRCC
Genatlas (Paris)PRCC
WikiGenes5546
SOURCE (Princeton)PRCC
Genomic and cartography
GoldenPath hg19 (UCSC)PRCC  -     chr1:156737274-156770609 +  1q21.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PRCC  -     1q21.1   [Description]    (hg38-Dec_2013)
EnsemblPRCC - 1q21.1 [CytoView hg19]  PRCC - 1q21.1 [CytoView hg38]
Mapping of homologs : NCBIPRCC [Mapview hg19]  PRCC [Mapview hg38]
OMIM179755   605074   
Gene and transcription
Genbank (Entrez)AA846273 AK126403 AK289872 BC004913 BC010450
RefSeq transcript (Entrez)NM_005973 NM_199416
RefSeq genomic (Entrez)NC_000001 NC_018912 NG_008138 NT_004487 NW_004929293
Consensus coding sequences : CCDS (NCBI)PRCC
Cluster EST : UnigeneHs.516948 [ NCBI ]
CGAP (NCI)Hs.516948
Alternative Splicing GalleryENSG00000143294
Gene ExpressionPRCC [ NCBI-GEO ]   PRCC [ EBI - ARRAY_EXPRESS ]   PRCC [ SEEK ]   PRCC [ MEM ]
Gene Expression Viewer (FireBrowse)PRCC [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5546
GTEX Portal (Tissue expression)PRCC
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ92733 (Uniprot)
NextProtQ92733  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ92733
Splice isoforms : SwissVarQ92733 (Swissvar)
PhosPhoSitePlusQ92733
Domains : Interpro (EBI)PRCC   
Domain families : Pfam (Sanger)PRCC (PF10253)   
Domain families : Pfam (NCBI)pfam10253   
DMDM Disease mutations5546
Blocks (Seattle)PRCC
SuperfamilyQ92733
Human Protein AtlasENSG00000143294
Peptide AtlasQ92733
HPRD01562
IPIIPI00294618   IPI00399306   IPI00514697   
Protein Interaction databases
DIP (DOE-UCLA)Q92733
IntAct (EBI)Q92733
FunCoupENSG00000143294
BioGRIDPRCC
STRING (EMBL)PRCC
ZODIACPRCC
Ontologies - Pathways
QuickGOQ92733
Ontology : AmiGOprotein binding  nucleus  mitotic cell cycle checkpoint  
Ontology : EGO-EBIprotein binding  nucleus  mitotic cell cycle checkpoint  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkPRCC
Atlas of Cancer Signalling NetworkPRCC
Wikipedia pathwaysPRCC
Orthology - Evolution
OrthoDB5546
GeneTree (enSembl)ENSG00000143294
Phylogenetic Trees/Animal Genes : TreeFamPRCC
Homologs : HomoloGenePRCC
Homology/Alignments : Family Browser (UCSC)PRCC
Gene fusions - Rearrangements
Fusion : MitelmanPRCC/HAPLN2 [1q23.1/1q23.1]  
Fusion : MitelmanPRCC/TFE3 [1q23.1/Xp11.23]  [t(X;1)(p11;q23)]  
Fusion : MitelmanPRCC/TMED5 [1q23.1/1p22.1]  [t(1;1)(p22;q23)]  
Fusion : COSMICTFE3 [Xp11.23]  -  PRCC [1q23.1]  [fusion_839]  [fusion_874]  
Fusion: TCGAPRCC 1q23.1 HAPLN2 1q23.1 BRCA
Fusion: TCGAPRCC 1q23.1 TMED5 1p22.1 THCA
Fusion : TICdbARHGAP6 [Xp22.2]  -  PRCC [1q23.1]
Polymorphisms : SNP, variants
NCBI Variation ViewerPRCC [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRCC
dbVarPRCC
ClinVarPRCC
1000_GenomesPRCC 
Exome Variant ServerPRCC
ExAC (Exome Aggregation Consortium)PRCC (select the gene name)
Genetic variants : HAPMAP5546
Genomic Variants (DGV)PRCC [DGVbeta]
Mutations
ICGC Data PortalPRCC 
TCGA Data PortalPRCC 
Broad Tumor PortalPRCC
OASIS PortalPRCC [ Somatic mutations - Copy number]
Cancer Gene: CensusPRCC 
Somatic Mutations in Cancer : COSMICPRCC 
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 PRCC
DgiDB (Drug Gene Interaction Database)PRCC
DoCM (Curated mutations)PRCC (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRCC (select a term)
intoGenPRCC
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)1:156737274-156770609  ENSG00000143294
CONAN: Copy Number AnalysisPRCC 
Mutations and Diseases : HGMDPRCC
OMIM179755    605074   
MedgenPRCC
Genetic Testing Registry PRCC
NextProtQ92733 [Medical]
TSGene5546
GENETestsPRCC
Huge Navigator PRCC [HugePedia]
snp3D : Map Gene to Disease5546
BioCentury BCIQPRCC
ClinGenPRCC
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5546
Chemical/Pharm GKB GenePA33704
Clinical trialPRCC
Miscellaneous
canSAR (ICR)PRCC (select the gene name)
Probes
Litterature
PubMed27 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRCC
EVEXPRCC
GoPubMedPRCC
iHOPPRCC
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 19 19:24:17 CEST 2016
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