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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)


Alias_symbol (synonym)HEPTP
Other aliasBPTP-4
LocusID (NCBI) 5778
Atlas_Id 41921
Location 1q32.1  [Link to chromosome band 1q32]
Location_base_pair Starts at 202147013 and ends at 202161588 bp from pter ( according to hg19-Feb_2009)  [Mapping PTPN7.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ADARB2 (10p15.3) / PTPN7 (1q32.1)PTPN7 (1q32.1) / PTPN7 (1q32.1)


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.


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).


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

Implicated in

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.


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


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 :

External links

HGNC (Hugo)PTPN7   9659
Entrez_Gene (NCBI)PTPN7  5778  protein tyrosine phosphatase, non-receptor type 7
GeneCards (Weizmann)PTPN7
Ensembl hg19 (Hinxton)ENSG00000143851 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000143851 [Gene_View]  chr1:202147013-202161588 [Contig_View]  PTPN7 [Vega]
ICGC DataPortalENSG00000143851
TCGA cBioPortalPTPN7
Genatlas (Paris)PTPN7
SOURCE (Princeton)PTPN7
Genetics Home Reference (NIH)PTPN7
Genomic and cartography
GoldenPath hg38 (UCSC)PTPN7  -     chr1:202147013-202161588 -  1q32.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PTPN7  -     1q32.1   [Description]    (hg19-Feb_2009)
EnsemblPTPN7 - 1q32.1 [CytoView hg19]  PTPN7 - 1q32.1 [CytoView hg38]
Mapping of homologs : NCBIPTPN7 [Mapview hg19]  PTPN7 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AF394064 AK127214 AK225920 AK293186 AK301051
RefSeq transcript (Entrez)NM_001199797 NM_002832 NM_080588 NM_080589
RefSeq genomic (Entrez)
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]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5778
GTEX Portal (Tissue expression)PTPN7
Human Protein AtlasENSG00000143851-PTPN7 [pathology]   [cell]   [tissue]
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 ] [ IntEnz-EBI ] [ BRENDA ] [ KEGG ]   
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_cat    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)  PTPc_motif (SM00404)  
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   
Human Protein Atlas [tissue]ENSG00000143851-PTPN7 [tissue]
Peptide AtlasP35236
IPIIPI00946771   IPI00081833   IPI01014710   IPI01016061   IPI00910869   IPI00514108   IPI00945123   IPI00944944   IPI00947394   IPI00947556   IPI00945382   IPI00514420   IPI00947371   IPI00947284   IPI00945424   IPI00945313   
Protein Interaction databases
IntAct (EBI)P35236
Ontologies - Pathways
Ontology : AmiGOprotein tyrosine phosphatase activity  protein binding  cytoplasm  cytosol  cytoskeleton  protein dephosphorylation  cytoplasmic side of plasma membrane  peptidyl-tyrosine dephosphorylation  
Ontology : EGO-EBIprotein tyrosine phosphatase activity  protein binding  cytoplasm  cytosol  cytoskeleton  protein dephosphorylation  cytoplasmic side of plasma membrane  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
GeneTree (enSembl)ENSG00000143851
Phylogenetic Trees/Animal Genes : TreeFamPTPN7
Homologs : HomoloGenePTPN7
Homology/Alignments : Family Browser (UCSC)PTPN7
Gene fusions - Rearrangements
Fusion : QuiverPTPN7
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPTPN7 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPN7
Exome Variant ServerPTPN7
ExAC (Exome Aggregation Consortium)ENSG00000143851
GNOMAD BrowserENSG00000143851
Genetic variants : HAPMAP5778
Genomic Variants (DGV)PTPN7 [DGVbeta]
DECIPHERPTPN7 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPTPN7 
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)
NCG5 (London)PTPN7
Cancer3DPTPN7(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry PTPN7
NextProtP35236 [Medical]
Target ValidationPTPN7
Huge Navigator PTPN7 [HugePedia]
snp3D : Map Gene to Disease5778
BioCentury BCIQPTPN7
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5778
Chemical/Pharm GKB GenePA34003
Clinical trialPTPN7
canSAR (ICR)PTPN7 (select the gene name)
PubMed30 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 5 12:42:56 CET 2018

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