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PTPN7 (protein tyrosine phosphatase, non-receptor type 7)

Written2010-01Marie Fridberg, Helena Tassidis, Anette Gjörloff Wingren
Department of Tumor Biology, Lund University, Malmo University Hospital, Malmo, Sweden (MF, HT); Department of Laboratory Science, Health, Society, Malmo University, Malmo University Hospital, Malmo, Sweden (AGW)

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)HEPTP
LC-PTP
HGNC (Hugo) PTPN7
LocusID (NCBI) 5778
Atlas_Id 41921
Location 1q32.1  [Link to chromosome band 1q32]
Location_base_pair Starts at 202116141 and ends at 202130716 bp from pter ( according to hg19-Feb_2009)  [Mapping PTPN7.png]
Fusion genes
(updated 2016)
ADARB2 (10p15.3) / PTPN7 (1q32.1)PTPN7 (1q32.1) / PTPN7 (1q32.1)

DNA/RNA

Description The premessenger has 10 exons and covers 14.59 kb on the genome.
Transcription The complete mRNA is 3784 bp long. 2 alternatively spliced transcript variants encoding different isoforms have been found, but it has also been reported that transcription produces 16 different mRNAs, 15 alternatively spliced variants and 1 unspliced form. Of the 2 described variants, variant 1 (2,805 bp linear mRNA) contains a different 5' region, which includes a part of the coding sequence when compared to variant 2. Variant 2 (3,263 bp linear mRNA) contains an alternate 5' region, which includes an additional in-frame translation start codon, as compared to variant 1. It thus encodes a protein that is 39 aa longer at the N-terminus.
Pseudogene No pseudogenes have been found.

Protein

Description The hematopoietic protein tyrosine phosphatase (HePTP) protein is a 40,5 kDa protein of 360 amino acids. It is a class I non-receptor PTP that is strongly expressed in T cells. It is composed of a C-terminal classical PTP domain (residues 44-339) and a short N-terminal extension (residues 1-43) that functions to direct HePTP to its physiological substrates.
Expression Thymus, spleen, leukocytes.
Localisation Cytoplasmic.
Function Protein tyrosine phosphatase activity, hydrolase activity, phosphoric monoester hydrolase activity, receptor activity- participation in MAPK signaling pathways, T cell receptor signaling pathway and protein amino acid dephosphorylation.
The protein can interact with tyrosine-phosphorylated MAPK1, MAPK3 and several other MAP kinases and suppress the MAP kinase activities. Plays a role in the regulation of T and B-lymphocyte development and signal transduction.
Homology HePTP has high homologies with striatal-enriched phosphatase (STEP) and PCPTP (PC12 protein Tyr phosphatase).

Mutations

Germinal No germline mutations are described.
Somatic Mutations have not been observed.

Implicated in

Note
Entity Acute leukemia
Disease Myelodysplastic syndrome and myelogenous leukemia; HePTP often is dysregulated in the preleukemic disorder myelodysplastic syndrome and myelogenous leukemia (elevated expression of HePTP). The first indication of a role of HePTP in cell proliferation or differentiation came from the finding that the HePTP gene is located on the long arm of chromosome 1, which is often found in extra copies (trisomy) in bone marrow cells from patients with myelodysplastic syndrome, which is characterized by reduced hematopoiesis and increased risk of acute leukemia.
  
Entity Non-Hodgkin Lymphoma
Disease Pediatric lymphoma; HePTP is down-regulated in pediatric lymphoma compared to control lymphoid cells. Loss of HePTP might indicate increased cell proliferation and/or survival of lymphoma cells.
  

Bibliography

Structure of the human LC-PTP (HePTP) gene: similarity in genomic organization within protein-tyrosine phosphatase genes.
Adachi M, Miyachi T, Sekiya M, Hinoda Y, Yachi A, Imai K.
Oncogene. 1994 Oct;9(10):3031-5.
PMID 8084610
 
Immunohistochemical analyses of phosphatases in childhood B-cell lymphoma: lower expression of PTEN and HePTP and higher number of positive cells for nuclear SHP2 in B-cell lymphoma cases compared to controls.
Fridberg M, Kjellstrom S, Anagnostaki L, Skogvall I, Mustelin T, Wiebe T, Persson JL, Dictor M, Wingren AG.
Pediatr Hematol Oncol. 2008 Sep;25(6):528-40.
PMID 18728972
 
Subcellular localization of intracellular protein tyrosine phosphatases in T cells.
Gjorloff-Wingren A, Saxena M, Han S, Wang X, Alonso A, Renedo M, Oh P, Williams S, Schnitzer J, Mustelin T.
Eur J Immunol. 2000 Aug;30(8):2412-21.
PMID 10940933
 
Structure of the hematopoietic tyrosine phosphatase (HePTP) catalytic domain: structure of a KIM phosphatase with phosphate bound at the active site.
Mustelin T, Tautz L, Page R.
J Mol Biol. 2005 Nov 18;354(1):150-63. Epub 2005 Oct 3.
PMID 16226275
 
Direct suppression of TCR-mediated activation of extracellular signal-regulated kinase by leukocyte protein tyrosine phosphatase, a tyrosine-specific phosphatase.
Oh-hora M, Ogata M, Mori Y, Adachi M, Imai K, Kosugi A, Hamaoka T.
J Immunol. 1999 Aug 1;163(3):1282-8.
PMID 10415025
 
The MAP-kinase ERK2 is a specific substrate of the protein tyrosine phosphatase HePTP.
Pettiford SM, Herbst R.
Oncogene. 2000 Feb 17;19(7):858-69.
PMID 10702794
 
Inhibition of T cell signaling by mitogen-activated protein kinase-targeted hematopoietic tyrosine phosphatase (HePTP).
Saxena M, Williams S, Brockdorff J, Gilman J, Mustelin T.
J Biol Chem. 1999 Apr 23;274(17):11693-700.
PMID 10206983
 
Cloning and expression of PCPTP1 encoding protein tyrosine phosphatase.
Shiozuka K, Watanabe Y, Ikeda T, Hashimoto S, Kawashima H.
Gene. 1995 Sep 11;162(2):279-84.
PMID 7557444
 
A hematopoietic protein tyrosine phosphatase (HePTP) gene that is amplified and overexpressed in myeloid malignancies maps to chromosome 1q32.1.
Zanke B, Squire J, Griesser H, Henry M, Suzuki H, Patterson B, Minden M, Mak TW.
Leukemia. 1994 Feb;8(2):236-44.
PMID 8309248
 
Cloning and expression of an inducible lymphoid-specific, protein tyrosine phosphatase (HePTPase).
Zanke B, Suzuki H, Kishihara K, Mizzen L, Minden M, Pawson A, Mak TW.
Eur J Immunol. 1992 Jan;22(1):235-9.
PMID 1530918
 

Citation

This paper should be referenced as such :
Fridberg, M ; Tassidis, H ; Gjörloff, Wingren A
PTPN7 (protein tyrosine phosphatase, non-receptor type 7)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(11):1032-1033.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PTPN7ID41921ch1q32.html


External links

Nomenclature
HGNC (Hugo)PTPN7   9659
Cards
AtlasPTPN7ID41921ch1q32
Entrez_Gene (NCBI)PTPN7  5778  protein tyrosine phosphatase, non-receptor type 7
AliasesBPTP-4; HEPTP; LC-PTP; LPTP; 
PTPNI
GeneCards (Weizmann)PTPN7
Ensembl hg19 (Hinxton)ENSG00000143851 [Gene_View]  chr1:202116141-202130716 [Contig_View]  PTPN7 [Vega]
Ensembl hg38 (Hinxton)ENSG00000143851 [Gene_View]  chr1:202116141-202130716 [Contig_View]  PTPN7 [Vega]
ICGC DataPortalENSG00000143851
TCGA cBioPortalPTPN7
AceView (NCBI)PTPN7
Genatlas (Paris)PTPN7
WikiGenes5778
SOURCE (Princeton)PTPN7
Genetics Home Reference (NIH)PTPN7
Genomic and cartography
GoldenPath hg19 (UCSC)PTPN7  -     chr1:202116141-202130716 -  1q32.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PTPN7  -     1q32.1   [Description]    (hg38-Dec_2013)
EnsemblPTPN7 - 1q32.1 [CytoView hg19]  PTPN7 - 1q32.1 [CytoView hg38]
Mapping of homologs : NCBIPTPN7 [Mapview hg19]  PTPN7 [Mapview hg38]
OMIM176889   
Gene and transcription
Genbank (Entrez)AF394064 AK127214 AK225920 AK293186 AK301051
RefSeq transcript (Entrez)NM_001199797 NM_002832 NM_080588 NM_080589
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_004487 NW_004929293
Consensus coding sequences : CCDS (NCBI)PTPN7
Cluster EST : UnigeneHs.402773 [ NCBI ]
CGAP (NCI)Hs.402773
Alternative Splicing GalleryENSG00000143851
Gene ExpressionPTPN7 [ NCBI-GEO ]   PTPN7 [ EBI - ARRAY_EXPRESS ]   PTPN7 [ SEEK ]   PTPN7 [ MEM ]
Gene Expression Viewer (FireBrowse)PTPN7 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5778
GTEX Portal (Tissue expression)PTPN7
Protein : pattern, domain, 3D structure
UniProt/SwissProtP35236   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP35236  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP35236
Splice isoforms : SwissVarP35236
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 ]   
PhosPhoSitePlusP35236
Domaine pattern : Prosite (Expaxy)TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (EBI)Prot-tyrosine_phosphatase-like    PTPase_domain    Tyr_Pase_AS    Tyr_Pase_KIM-con    TYR_PHOSPHATASE_dom   
Domain families : Pfam (Sanger)Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam00102   
Domain families : Smart (EMBL)PTPc (SM00194)  
Conserved Domain (NCBI)PTPN7
DMDM Disease mutations5778
Blocks (Seattle)PTPN7
PDB (SRS)1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
PDB (PDBSum)1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
PDB (IMB)1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
PDB (RSDB)1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
Structural Biology KnowledgeBase1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
SCOP (Structural Classification of Proteins)1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
CATH (Classification of proteins structures)1ZC0    2A3K    2GP0    2GPH    2HVL    2QDC    2QDM    2QDP    3D42    3D44    3O4S    3O4T    3O4U   
SuperfamilyP35236
Human Protein AtlasENSG00000143851
Peptide AtlasP35236
HPRD01480
IPIIPI00946771   IPI00081833   IPI01014710   IPI01016061   IPI00910869   IPI00514108   IPI00945123   IPI00944944   IPI00947394   IPI00947556   IPI00945382   IPI00514420   IPI00947371   IPI00947284   IPI00945424   IPI00945313   
Protein Interaction databases
DIP (DOE-UCLA)P35236
IntAct (EBI)P35236
FunCoupENSG00000143851
BioGRIDPTPN7
STRING (EMBL)PTPN7
ZODIACPTPN7
Ontologies - Pathways
QuickGOP35236
Ontology : AmiGOprotein tyrosine phosphatase activity  protein binding  cytoplasm  cytosol  cytoskeleton  protein dephosphorylation  cytoplasmic side of plasma membrane  peptidyl-tyrosine dephosphorylation  peptidyl-tyrosine dephosphorylation  
Ontology : EGO-EBIprotein tyrosine phosphatase activity  protein binding  cytoplasm  cytosol  cytoskeleton  protein dephosphorylation  cytoplasmic side of plasma membrane  peptidyl-tyrosine dephosphorylation  peptidyl-tyrosine dephosphorylation  
Pathways : BIOCARTAT Cell Receptor Signaling Pathway [Genes]   
Pathways : KEGGMAPK signaling pathway   
NDEx NetworkPTPN7
Atlas of Cancer Signalling NetworkPTPN7
Wikipedia pathwaysPTPN7
Orthology - Evolution
OrthoDB5778
GeneTree (enSembl)ENSG00000143851
Phylogenetic Trees/Animal Genes : TreeFamPTPN7
HOVERGENP35236
HOGENOMP35236
Homologs : HomoloGenePTPN7
Homology/Alignments : Family Browser (UCSC)PTPN7
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPTPN7 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPN7
dbVarPTPN7
ClinVarPTPN7
1000_GenomesPTPN7 
Exome Variant ServerPTPN7
ExAC (Exome Aggregation Consortium)PTPN7 (select the gene name)
Genetic variants : HAPMAP5778
Genomic Variants (DGV)PTPN7 [DGVbeta]
DECIPHER (Syndromes)1:202116141-202130716  ENSG00000143851
CONAN: Copy Number AnalysisPTPN7 
Mutations
ICGC Data PortalPTPN7 
TCGA Data PortalPTPN7 
Broad Tumor PortalPTPN7
OASIS PortalPTPN7 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPTPN7  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPTPN7
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 PTPN7
DgiDB (Drug Gene Interaction Database)PTPN7
DoCM (Curated mutations)PTPN7 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTPN7 (select a term)
intoGenPTPN7
NCG5 (London)PTPN7
Cancer3DPTPN7(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM176889   
Orphanet
MedgenPTPN7
Genetic Testing Registry PTPN7
NextProtP35236 [Medical]
TSGene5778
GENETestsPTPN7
Huge Navigator PTPN7 [HugePedia]
snp3D : Map Gene to Disease5778
BioCentury BCIQPTPN7
ClinGenPTPN7
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5778
Chemical/Pharm GKB GenePA34003
Clinical trialPTPN7
Miscellaneous
canSAR (ICR)PTPN7 (select the gene name)
Probes
Litterature
PubMed29 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTPN7
EVEXPTPN7
GoPubMedPTPN7
iHOPPTPN7
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Nov 18 20:02:09 CET 2016

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