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PTPN13 (Protein tyrosine phosphatase, non-receptor type 13)

Written2008-09Alessandro Beghini
University of Milan, Medical Faculty, Department of Biology, Genetics for Medical Sciences, via Viotti 5, 20133-Milan, Italy

(Note : for Links provided by Atlas : click)

Identity

Alias_namesprotein tyrosine phosphatase
Alias_symbol (synonym)PTP1E
PTP-BAS
PTPL1
PTP-BL
Other aliasDKFZp686J1497
FAP-1
PNP1
PTP-E1
PTPLE
HGNC (Hugo) PTPN13
LocusID (NCBI) 5783
Atlas_Id 41912
Location 4q21.3  [Link to chromosome band 4q21]
Location_base_pair Starts at 86594315 and ends at 86815175 bp from pter ( according to hg19-Feb_2009)  [Mapping PTPN13.png]
 
  Genomic view
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AFF1 (4q21.3) / PTPN13 (4q21.3)LRRC61 (7q36.1) / PTPN13 (4q21.3)MARCH1 (4q32.2) / PTPN13 (4q21.3)
PTPN13 (4q21.3) / PTPN13 (4q21.3)PTPN13 (4q21.3) / TUBA1A (12q13.12)TMEM63A (1q42.12) / PTPN13 (4q21.3)
TUBA1A (12q13.12) / PTPN13 (4q21.3)
Note Genomic context : PTPN13 lies in a head-to-head conformation with MAPK10/JNK3 and they share a 633bp bi-directional promoter which is a typical CpG island.

DNA/RNA

Description The gene covers 220.87 kb (from 87734485 to 87955350-NCBI) and contains 48 exons and 51 different introns (49 gt-ag, 2 gc-ag), initiates transcription within exon 2 and terminates in exon 48.
Transcription Transcription produces 13 different mRNAs, 9 alternatively spliced variants and 4 unspliced forms. RefSeq annotates 4 representative transcripts, but Homo sapiens cDNA sequences in GenBank support at least 9 spliced variants.

Protein

Description The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP is a large protein that possesses a PTP domain at C-terminus, and multiple noncatalytic domains, which include a domain with similarity to band 4.1 superfamily of cytoskeletal-associated proteins, a region consisting of five PDZ domains, and a leucine zipper motif. This PTP was found to interact with, and dephosphorylate Fas receptor, as well as IkappaBalpha through the PDZ domains, which suggested its role in Fas mediated programmed cell death. This PTP was also shown to interact with GTPase-activating protein, and thus may function as a regulator of Rho signaling pathway. Eight spliced and the unspliced mRNAs putatively encode good proteins.
 
  Schematic representation of PTPN13 structure and boxes represent functional domains. The KIND domain has been identified in silico by sequence homology.
Expression In all human normal tissues, including lymph node and peripheral blood mononuclear cells samples, PTPN13 is ubiquitously expressed.
Localisation The FERM domain binds to phosphatidylinositol 4,5-biphosphate leading to the enrichment of PTPN13 at a juxtamembrane localization. However, the PTPN13 protein is also detected throughout the cytoplasm. In HeLa cells, PTPN13 localizes to the centrosomes during metaphase.
Function Functionally, the gene has been tested for association to diseases (Bone Neoplasms; Carcinoma; Colorectal Neoplasms; Liver Neoplasms; lymphoma; Sarcoma, Ewing's ), proposed to participate in a pathway (FAS signaling pathway ( CD95 )) and a process (protein amino acid dephosphorylation). Proteins are expected to have molecular functions (non-membrane spanning protein tyrosine phosphatase activity, hydrolase activity, protein binding, structural molecule activity) and to localize in various compartments (nucleus, cytoplasm, cytoskeleton).

Mutations

Note Different somatic mutations was identified in colorectal tumors (19% of the colorectal cancer samples analyzed), predicted to result in missense or non-sense mutations. Some of these mutant proteins led to reduce phosphatase activity.
 
  Distribution of mutations in PTPN13, black arrows indicate location of missense mutations, red arrows indicate location of nonsense mutations or frameshifts.

Implicated in

Note
  
Entity Colorectal cancers
Disease A large-scale study that looked at the mutations in the tyrosine phosphatome from colorectal cancers identified PTPN13. The authors identified 19 mutations, non-sense and missense, seven of which were in the PTP domain.
  
  
Entity Lymphomas (Hodgkin and non-Hodgkin), gastric and hepatocellular tumors
Disease Hypermethylation of the PTPN13 promoter or allelic loss was observed leading to downregulation of PTPN13 mRNA.
  

To be noted

Several evidences suggest that PTPN13 may act differently as a tumor promoting gene depending upon the disease context. The modulation of Fas-mediated cell death by PTPN13 could enhance tumor growth by blocking death signaling.

Bibliography

PTPL1: a large phosphatase with a split personality.
Abaan OD, Toretsky JA.
Cancer Metastasis Rev. 2008 Jun; 27(2): 205-214. (Review)
PMID 18265946
 
A novel protein-tyrosine phosphatase with homology to both the cytoskeletal proteins of the band 4.1 family and junction-associated guanylate kinases.
Banville D, Ahmad S, Stocco R, Shen SH.
J. Biol. Chem. 1994; 269: 22320-22327.
PMID 8071359
 
PTPN13, a Fas-associated protein tyrosine phosphatase, is located on the long arm of chromosome 4 at band q21.3.
Inazawa J, Ariyama T, Abe T, Druck T, Ohta M, Huebner K, Yanagisawa J, Reed JC, Sato T.
Genomics 1996; 31: 240-242.
PMID 8824809
 
Molecular cloning of a novel protein-tyrosine phosphatase containing a membrane-binding domain and GLGF repeats.
Maekawa K, Imagawa N, Nagamatsu M, Harada S.
FEBS Lett. 1994; 337: 200-206.
PMID 8287977
 
Cloning and characterization of PTPL1, a protein tyrosine phosphatase with similarities to cytoskeletal-associated proteins.
Saras J, Claesson-Welsh L, Heldin CH, Gonez LJ.
J. Biol. Chem. 1994; 269: 24082-24089.
PMID 7929060
 
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 JKV, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE.
Science 2004; 304: 1164-1166.
PMID 15155950
 
Genetic characterization of fas-associated phosphatase-1 as a putative tumor suppressor gene on chromosome 4q21.3 in hepatocellular carcinoma.
Yeh SH, Wu DC, Tsai CY, Kuo TJ, Yu WC, Chang YS, Chen CL, Chang CF, Chen DS, Chen PJ.
Clin Cancer Res. 2006 Feb 15; 12(4): 1097-1108.
PMID 16489062
 
Epigenetic disruption of two proapoptotic genes MAPK10/JNK3 and PTPN13/FAP-1 in multiple lymphomas and carcinomas through hypermethylation of a common bidirectional promoter.
Ying J, Li H, Cui Y, Wong AH, Langford C, Tao Q.
Leukemia. 2006 Jun; 20(6): 1173-1175.
PMID 16572203
 
Head-to-head juxtaposition of Fas-associated phosphatase-1 (FAP-1) and c-Jun NH2-terminal kinase 3 (JNK3) genes: genomic structure and seven polymorphisms of the FAP-1 gene.
Yoshida S, Harada H, Nagai H, Fukino K, Teramoto A, Emi M.
J. Hum. Genet. 2002; 47: 614-619.
PMID 12436199
 
The gene (PTPN13) encoding the protein tyrosine phosphatase PTP-BL/PTP-BAS is located in mouse chromosome region 5E/F and human chromosome region 4q21.
van den Maagdenberg AM, Olde Weghuis D, Rijss J, Merkx GF, Wieringa B, Geurts van Kessel A, Hendriks WJ.
Cytogenet. Cell Genet. 1996; 74: 153-155.
PMID 8893825
 

Citation

This paper should be referenced as such :
Beghini, A
PTPN13 (Protein tyrosine phosphatase, non-receptor type 13)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(8):573-575.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PTPN13ID41912ch4q21.html


External links

Nomenclature
HGNC (Hugo)PTPN13   9646
Cards
AtlasPTPN13ID41912ch4q21
Entrez_Gene (NCBI)PTPN13  5783  protein tyrosine phosphatase, non-receptor type 13
AliasesFAP-1; PNP1; PTP-BAS; PTP-BL; 
PTP1E; PTPL1; PTPLE; hPTP1E
GeneCards (Weizmann)PTPN13
Ensembl hg19 (Hinxton)ENSG00000163629 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000163629 [Gene_View]  chr4:86594315-86815175 [Contig_View]  PTPN13 [Vega]
ICGC DataPortalENSG00000163629
TCGA cBioPortalPTPN13
AceView (NCBI)PTPN13
Genatlas (Paris)PTPN13
WikiGenes5783
SOURCE (Princeton)PTPN13
Genetics Home Reference (NIH)PTPN13
Genomic and cartography
GoldenPath hg38 (UCSC)PTPN13  -     chr4:86594315-86815175 +  4q21.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PTPN13  -     4q21.3   [Description]    (hg19-Feb_2009)
EnsemblPTPN13 - 4q21.3 [CytoView hg19]  PTPN13 - 4q21.3 [CytoView hg38]
Mapping of homologs : NCBIPTPN13 [Mapview hg19]  PTPN13 [Mapview hg38]
OMIM600267   
Gene and transcription
Genbank (Entrez)AB208904 AF233323 AK056151 BC039610 BC139915
RefSeq transcript (Entrez)NM_006264 NM_080683 NM_080684 NM_080685
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PTPN13
Cluster EST : UnigeneHs.436142 [ NCBI ]
CGAP (NCI)Hs.436142
Alternative Splicing GalleryENSG00000163629
Gene ExpressionPTPN13 [ NCBI-GEO ]   PTPN13 [ EBI - ARRAY_EXPRESS ]   PTPN13 [ SEEK ]   PTPN13 [ MEM ]
Gene Expression Viewer (FireBrowse)PTPN13 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5783
GTEX Portal (Tissue expression)PTPN13
Human Protein AtlasENSG00000163629-PTPN13 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ12923   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ12923  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ12923
Splice isoforms : SwissVarQ12923
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 ]   
PhosPhoSitePlusQ12923
Domaine pattern : Prosite (Expaxy)FERM_3 (PS50057)    KIND (PS51377)    PDZ (PS50106)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (EBI)Band_41_domain    FERM/acyl-CoA-bd_prot_3-hlx    FERM_central    FERM_domain    FERM_N    FERM_PH-like_C    KIND_dom    PDZ    PH_dom-like    Prot-tyrosine_phosphatase-like    PTPase_domain    PTPN13    Tyr_Pase_cat    TYR_PHOSPHATASE_dom    Ubiquitin-rel_dom   
Domain families : Pfam (Sanger)FERM_C (PF09380)    FERM_M (PF00373)    FERM_N (PF09379)    PDZ (PF00595)    Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam09380    pfam00373    pfam09379    pfam00595    pfam00102   
Domain families : Smart (EMBL)B41 (SM00295)  FERM_C (SM01196)  KIND (SM00750)  PDZ (SM00228)  PTPc (SM00194)  PTPc_motif (SM00404)  
Conserved Domain (NCBI)PTPN13
DMDM Disease mutations5783
Blocks (Seattle)PTPN13
PDB (SRS)1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
PDB (PDBSum)1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
PDB (IMB)1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
PDB (RSDB)1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
Structural Biology KnowledgeBase1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
SCOP (Structural Classification of Proteins)1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
CATH (Classification of proteins structures)1D5G    1Q7X    1WCH    2M0Z    2M10    3LNX    3LNY    3PDZ    5GLJ   
SuperfamilyQ12923
Human Protein Atlas [tissue]ENSG00000163629-PTPN13 [tissue]
Peptide AtlasQ12923
HPRD02602
IPIIPI00030246   IPI00472958   IPI00006714   IPI00337648   IPI01015899   IPI00964104   IPI00965009   
Protein Interaction databases
DIP (DOE-UCLA)Q12923
IntAct (EBI)Q12923
FunCoupENSG00000163629
BioGRIDPTPN13
STRING (EMBL)PTPN13
ZODIACPTPN13
Ontologies - Pathways
QuickGOQ12923
Ontology : AmiGOprotein tyrosine phosphatase activity  protein tyrosine phosphatase activity  protein binding  nucleus  cytoplasm  cytoskeleton  plasma membrane  plasma membrane  protein dephosphorylation  phosphatidylinositol biosynthetic process  regulation of phosphatidylinositol 3-kinase signaling  lamellipodium  peptidyl-tyrosine dephosphorylation  phosphatidylinositol 3-kinase regulatory subunit binding  neuron projection  cell body  extracellular exosome  
Ontology : EGO-EBIprotein tyrosine phosphatase activity  protein tyrosine phosphatase activity  protein binding  nucleus  cytoplasm  cytoskeleton  plasma membrane  plasma membrane  protein dephosphorylation  phosphatidylinositol biosynthetic process  regulation of phosphatidylinositol 3-kinase signaling  lamellipodium  peptidyl-tyrosine dephosphorylation  phosphatidylinositol 3-kinase regulatory subunit binding  neuron projection  cell body  extracellular exosome  
Pathways : BIOCARTAFAS signaling pathway ( CD95 ) [Genes]   
REACTOMEQ12923 [protein]
REACTOME PathwaysR-HSA-1660499 [pathway]   
NDEx NetworkPTPN13
Atlas of Cancer Signalling NetworkPTPN13
Wikipedia pathwaysPTPN13
Orthology - Evolution
OrthoDB5783
GeneTree (enSembl)ENSG00000163629
Phylogenetic Trees/Animal Genes : TreeFamPTPN13
HOVERGENQ12923
HOGENOMQ12923
Homologs : HomoloGenePTPN13
Homology/Alignments : Family Browser (UCSC)PTPN13
Gene fusions - Rearrangements
Fusion : MitelmanAFF1/PTPN13 [4q21.3/4q21.3]  [t(4;4)(q21;q21)]  
Fusion : MitelmanMARCH1/PTPN13 [4q32.2/4q21.3]  [t(4;4)(q21;q32)]  
Fusion : MitelmanTUBA1A/PTPN13 [12q13.12/4q21.3]  [t(4;12)(q21;q13)]  
Fusion: TCGA_MDACCAFF1 4q21.3 PTPN13 4q21.3 BLCA LUAD LUSC
Fusion: TCGA_MDACCMARCH1 4q32.2 PTPN13 4q21.3 LUSC
Tumor Fusion PortalPTPN13
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPTPN13 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPN13
dbVarPTPN13
ClinVarPTPN13
1000_GenomesPTPN13 
Exome Variant ServerPTPN13
ExAC (Exome Aggregation Consortium)ENSG00000163629
GNOMAD BrowserENSG00000163629
Genetic variants : HAPMAP5783
Genomic Variants (DGV)PTPN13 [DGVbeta]
DECIPHERPTPN13 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPTPN13 
Mutations
ICGC Data PortalPTPN13 
TCGA Data PortalPTPN13 
Broad Tumor PortalPTPN13
OASIS PortalPTPN13 [ Somatic mutations - Copy number]
Cancer Gene: CensusPTPN13 
Somatic Mutations in Cancer : COSMICPTPN13  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPTPN13
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 PTPN13
DgiDB (Drug Gene Interaction Database)PTPN13
DoCM (Curated mutations)PTPN13 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTPN13 (select a term)
intoGenPTPN13
NCG5 (London)PTPN13
Cancer3DPTPN13(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600267   
Orphanet
DisGeNETPTPN13
MedgenPTPN13
Genetic Testing Registry PTPN13
NextProtQ12923 [Medical]
TSGene5783
GENETestsPTPN13
Target ValidationPTPN13
Huge Navigator PTPN13 [HugePedia]
snp3D : Map Gene to Disease5783
BioCentury BCIQPTPN13
ClinGenPTPN13
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5783
Chemical/Pharm GKB GenePA33988
Clinical trialPTPN13
Miscellaneous
canSAR (ICR)PTPN13 (select the gene name)
Probes
Litterature
PubMed101 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTPN13
EVEXPTPN13
GoPubMedPTPN13
iHOPPTPN13
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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