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PTPRG (protein tyrosine phosphatase, receptor type, G)

Written2006-12Cornelis P Tensen, Remco van Doorn
Departments of Dermatology and Medical Statistics, Leiden University Medical Center, Leiden, the Netherlands

(Note : for Links provided by Atlas : click)

Identity

Other namesHPTPG
PTPG
R-PTP-GAMMA
RPTPG
HGNC (Hugo) PTPRG
LocusID (NCBI) 5793
Atlas_Id 41930
Location 3p14.2  [Link to chromosome band 3p14]
Location_base_pair Starts at 61547243 and ends at 62280573 bp from pter ( according to hg19-Feb_2009)  [Mapping PTPRG.png]
Fusion genes
(updated 2016)
ASTN2 (9q33.1) / PTPRG (3p14.2)CELF2 (10p14) / PTPRG (3p14.2)FHIT (3p14.2) / PTPRG (3p14.2)
PTPRG (3p14.2) / FHIT (3p14.2)PTPRG (3p14.2) / LOC100294362 (17q25.3)PTPRG (3p14.2) / MCM3AP (21q22.3)
PTPRG (3p14.2) / PRPF4B (6p25.2)PTPRG (3p14.2) / PTPRG (3p14.2)PTPRG (3p14.2) / SYNPR (3p14.2)
PTPRG (3p14.2) / ZNF236 (18q23)PTPRG (3p14.2) / ZNF546 (19q13.2)SCYL2 (12q23.1) / PTPRG (3p14.2)
TRPC1 (3q23) / PTPRG (3p14.2)VWA8 (13q14.11) / PTPRG (3p14.2)

DNA/RNA

Description The PTPRG gene is composed of 30 exons and is approximately 780 kb in size.
Transcription The transcript length is 4338 bp. An alternatively spliced variant has been reported with a transcript length of 5655 bp.
Pseudogene no pseudogenes have been reported.

Protein

Description Amino acids: 1445. Molecular weight: 162058 Daltons. The PTPRG gene belongs to the receptor class 5 subfamily of the protein-tyrosine phosphatase family.
Expression PTPRG is expressed in several tissues.
Localisation Membrane. Single-pass type I membrane protein.
Function Involved in regulating signaling through ligand-controlled protein tyrosine dephosphorylation. The protein contains an extracellular carbonic anhydrase-like and fibronectin type III-like domain, a single transmembrane domain, and a cytoplasmic region with 2 tandem catalytic tyrosine phosphatase domains. Y2H, animal models.
Homology PTPRG shares a PTP domain, involved in dephosphorylating phosphorylated tyrosine residues, with the other receptor-like protein tyrosine phosphatases. The PTPRG gene is conserved in vertebrates. The human and mouse (1442-amino acid) sequences share 95% identity at the amino acid level.

Mutations

Germinal No germline mutations have been reported.
Somatic 8 different missense mutations in the PTPRG gene have been identified in colon carcinomas: C1082T (T361M), C1385T (A462V), C1541T (T514M), C1777T (R593W), A2864G (E955G), A2918G (Y973C), C3934T (R1312W) A3976G (I1326V).
Loss of heterozygosity (LOH) of a region which includes the PTPRG locus has been shown in clear renal cell carcinoma, lung carcinoma and colon carcinoma.

Implicated in

Note
Note PTPRG has been considered a potential tumor suppressor gene based on its function, antagonizing activity of protein tyrosine kinases that often function as oncoproteins. Secondly, because it maps to a region of human chromosome 3, 3p21, that is frequently deleted in renal cell carcinoma and Lung carcinoma. Thirdly, because PTPRG has been shown to harbor point mutations in a subset of colon carcinomas. Fourthly, because the PTPRG gene shows promoter hypermethylation in cutaneous T-cell lymphoma and melanoma. Finally, lower expression levels of PTPRG have been reported for a number of cancerous tissues including gastric cancer.
  

Bibliography

Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas.
Furuta J, Nobeyama Y, Umebayashi Y, Otsuka F, Kikuchi K, Ushijima T
Cancer research. 2006 ; 66 (12) : 6080-6086.
PMID 16778180
 
Receptor protein-tyrosine phosphatase gamma is a candidate tumor suppressor gene at human chromosome region 3p21.
LaForgia S, Morse B, Levy J, Barnea G, Cannizzaro LA, Li F, Nowell PC, Boghosian-Sell L, Glick J, Weston A
Proceedings of the National Academy of Sciences of the United States of America. 1991 ; 88 (11) : 5036-5040.
PMID 1711217
 
Mutational analysis of the tyrosine phosphatome in colorectal cancers.
Wang Z, Shen D, Parsons DW, Bardelli A, Sager J, Szabo S, Ptak J, Silliman N, Peters BA, van der Heijden MS, Parmigiani G, Yan H, Wang TL, Riggins G, Powell SM, Willson JK, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE
Science (New York, N.Y.). 2004 ; 304 (5674) : 1164-1166.
PMID 15155950
 
Protein tyrosine-phosphatase expression profiling in gastric cancer tissues.
Wu CW, Kao HL, Li AF, Chi CW, Lin WC
Cancer letters. 2006 ; 242 (1) : 95-103.
PMID 16338072
 
Epigenetic profiling of cutaneous T-cell lymphoma: promoter hypermethylation of multiple tumor suppressor genes including BCL7a, PTPRG, and p73.
van Doorn R, Zoutman WH, Dijkman R, de Menezes RX, Commandeur S, Mulder AA, van der Velden PA, Vermeer MH, Willemze R, Yan PS, Huang TH, Tensen CP
Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2005 ; 23 (17) : 3886-3896.
PMID 15897551
 

Citation

This paper should be referenced as such :
van, Doorn R ; Tensen, CP
PTPRG (protein tyrosine phosphatase, receptor type, G)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(2):107-108.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PTPRGID41930ch3p21.html


External links

Nomenclature
HGNC (Hugo)PTPRG   9671
Cards
AtlasPTPRGID41930ch3p21
Entrez_Gene (NCBI)PTPRG  5793  protein tyrosine phosphatase, receptor type G
AliasesHPTPG; PTPG; R-PTP-GAMMA; RPTPG
GeneCards (Weizmann)PTPRG
Ensembl hg19 (Hinxton)ENSG00000144724 [Gene_View]  chr3:61547243-62280573 [Contig_View]  PTPRG [Vega]
Ensembl hg38 (Hinxton)ENSG00000144724 [Gene_View]  chr3:61547243-62280573 [Contig_View]  PTPRG [Vega]
ICGC DataPortalENSG00000144724
TCGA cBioPortalPTPRG
AceView (NCBI)PTPRG
Genatlas (Paris)PTPRG
WikiGenes5793
SOURCE (Princeton)PTPRG
Genomic and cartography
GoldenPath hg19 (UCSC)PTPRG  -     chr3:61547243-62280573 +  3p21-p14   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PTPRG  -     3p21-p14   [Description]    (hg38-Dec_2013)
EnsemblPTPRG - 3p21-p14 [CytoView hg19]  PTPRG - 3p21-p14 [CytoView hg38]
Mapping of homologs : NCBIPTPRG [Mapview hg19]  PTPRG [Mapview hg38]
OMIM176886   
Gene and transcription
Genbank (Entrez)AB209871 AI872451 AK296327 BC036018 BC047734
RefSeq transcript (Entrez)NM_002841
RefSeq genomic (Entrez)NC_000003 NC_018914 NT_022517 NW_004929309
Consensus coding sequences : CCDS (NCBI)PTPRG
Cluster EST : UnigeneHs.595541 [ NCBI ]
CGAP (NCI)Hs.595541
Alternative Splicing GalleryENSG00000144724
Gene ExpressionPTPRG [ NCBI-GEO ]   PTPRG [ EBI - ARRAY_EXPRESS ]   PTPRG [ SEEK ]   PTPRG [ MEM ]
Gene Expression Viewer (FireBrowse)PTPRG [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5793
GTEX Portal (Tissue expression)PTPRG
Protein : pattern, domain, 3D structure
UniProt/SwissProtP23470 (Uniprot)
NextProtP23470  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP23470
Splice isoforms : SwissVarP23470 (Swissvar)
Catalytic activity : Enzyme3.1.3.48 [ Enzyme-Expasy ]   3.1.3.483.1.3.48 [ IntEnz-EBI ]   3.1.3.48 [ BRENDA ]   3.1.3.48 [ KEGG ]   
PhosPhoSitePlusP23470
Domaine pattern : Prosite (Expaxy)ALPHA_CA_2 (PS51144)    FN3 (PS50853)    TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (EBI)Carbonic_anhydrase_a    FN3_dom    Ig-like_fold    Prot-tyrosine_phosphatase-like    PTPase_domain    Tyr_Pase_AS    TYR_PHOSPHATASE_dom   
Domain families : Pfam (Sanger)Carb_anhydrase (PF00194)    fn3 (PF00041)    Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam00194    pfam00041    pfam00102   
Domain families : Smart (EMBL)Carb_anhydrase (SM01057)  FN3 (SM00060)  PTPc (SM00194)  
DMDM Disease mutations5793
Blocks (Seattle)PTPRG
PDB (SRS)2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
PDB (PDBSum)2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
PDB (IMB)2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
PDB (RSDB)2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
Structural Biology KnowledgeBase2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
SCOP (Structural Classification of Proteins)2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
CATH (Classification of proteins structures)2H4V    2HY3    2NLK    2PBN    3JXH    3QCB    3QCC    3QCD    3QCE    3QCF    3QCG    3QCH    3QCI    3QCJ    3QCK    3QCL    3QCM    3QCN   
SuperfamilyP23470
Human Protein AtlasENSG00000144724
Peptide AtlasP23470
HPRD01478
IPIIPI00011651   IPI00796281   IPI00985082   IPI00641879   IPI00395867   
Protein Interaction databases
DIP (DOE-UCLA)P23470
IntAct (EBI)P23470
FunCoupENSG00000144724
BioGRIDPTPRG
STRING (EMBL)PTPRG
ZODIACPTPRG
Ontologies - Pathways
QuickGOP23470
Ontology : AmiGOprotein tyrosine phosphatase activity  transmembrane receptor protein tyrosine phosphatase activity  protein binding  integral component of plasma membrane  transmembrane receptor protein tyrosine kinase signaling pathway  negative regulation of epithelial cell migration  peptidyl-tyrosine dephosphorylation  peptidyl-tyrosine dephosphorylation  peptidyl-tyrosine dephosphorylation  identical protein binding  extracellular exosome  regulation of homophilic cell adhesion  
Ontology : EGO-EBIprotein tyrosine phosphatase activity  transmembrane receptor protein tyrosine phosphatase activity  protein binding  integral component of plasma membrane  transmembrane receptor protein tyrosine kinase signaling pathway  negative regulation of epithelial cell migration  peptidyl-tyrosine dephosphorylation  peptidyl-tyrosine dephosphorylation  peptidyl-tyrosine dephosphorylation  identical protein binding  extracellular exosome  regulation of homophilic cell adhesion  
NDEx Network
Atlas of Cancer Signalling NetworkPTPRG
Wikipedia pathwaysPTPRG
Orthology - Evolution
OrthoDB5793
GeneTree (enSembl)ENSG00000144724
Phylogenetic Trees/Animal Genes : TreeFamPTPRG
Homologs : HomoloGenePTPRG
Homology/Alignments : Family Browser (UCSC)PTPRG
Gene fusions - Rearrangements
Fusion : MitelmanASTN2/PTPRG [9q33.1/3p14.2]  [t(3;9)(p14;q33)]  
Fusion : MitelmanFHIT/PTPRG [3p14.2/3p14.2]  [t(3;3)(p14;p14)]  
Fusion : MitelmanPTPRG/FHIT [3p14.2/3p14.2]  [t(3;3)(p14;p14)]  
Fusion : MitelmanPTPRG/MCM3AP [3p14.2/21q22.3]  [t(3;21)(p14;q22)]  
Fusion : MitelmanPTPRG/SYNPR [3p14.2/3p14.2]  [t(3;3)(p14;p14)]  
Fusion : MitelmanTRPC1/PTPRG [3q23/3p14.2]  [t(3;3)(p14;q23)]  
Fusion : MitelmanVWA8/PTPRG [13q14.11/3p14.2]  [t(3;13)(p14;q14)]  
Fusion: TCGAFHIT 3p14.2 PTPRG 3p14.2 LGG
Fusion: TCGAKIAA0564 PTPRG 3p14.2 BRCA
Fusion: TCGAPTPRG 3p14.2 FHIT 3p14.2 BRCA PRAD
Fusion: TCGAPTPRG 3p14.2 MCM3AP 21q22.3 LUSC
Fusion: TCGAPTPRG 3p14.2 SYNPR 3p14.2 SKCM
Fusion: TCGATRPC1 3q23 PTPRG 3p14.2 KIRC
Polymorphisms : SNP, variants
NCBI Variation ViewerPTPRG [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPRG
dbVarPTPRG
ClinVarPTPRG
1000_GenomesPTPRG 
Exome Variant ServerPTPRG
ExAC (Exome Aggregation Consortium)PTPRG (select the gene name)
Genetic variants : HAPMAP5793
Genomic Variants (DGV)PTPRG [DGVbeta]
Mutations
ICGC Data PortalPTPRG 
TCGA Data PortalPTPRG 
Broad Tumor PortalPTPRG
OASIS PortalPTPRG [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPTPRG 
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 PTPRG
DgiDB (Drug Gene Interaction Database)PTPRG
DoCM (Curated mutations)PTPRG (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTPRG (select a term)
intoGenPTPRG
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)3:61547243-62280573  ENSG00000144724
CONAN: Copy Number AnalysisPTPRG 
Mutations and Diseases : HGMDPTPRG
OMIM176886   
MedgenPTPRG
Genetic Testing Registry PTPRG
NextProtP23470 [Medical]
TSGene5793
GENETestsPTPRG
Huge Navigator PTPRG [HugePedia]
snp3D : Map Gene to Disease5793
BioCentury BCIQPTPRG
ClinGenPTPRG
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5793
Chemical/Pharm GKB GenePA34016
Clinical trialPTPRG
Miscellaneous
canSAR (ICR)PTPRG (select the gene name)
Probes
Litterature
PubMed44 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTPRG
EVEXPTPRG
GoPubMedPTPRG
iHOPPTPRG
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Aug 10 18:51:09 CEST 2016

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