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    PTPN2 protein tyrosine phosphatase non-receptor type 2 [ Homo sapiens (human) ]

    Gene ID: 5771, updated on 19-Sep-2024

    Summary

    Official Symbol
    PTPN2provided by HGNC
    Official Full Name
    protein tyrosine phosphatase non-receptor type 2provided by HGNC
    Primary source
    HGNC:HGNC:9650
    See related
    Ensembl:ENSG00000175354 MIM:176887; AllianceGenome:HGNC:9650
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PTN2; PTPT; TC45; TC48; TCPTP; TC-PTP; TCELLPTP
    Summary
    The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. Members of the PTP family share a highly conserved catalytic motif, which is essential for the catalytic activity. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. Epidermal growth factor receptor and the adaptor protein Shc were reported to be substrates of this PTP, which suggested the roles in growth factor mediated cell signaling. Multiple alternatively spliced transcript variants encoding different isoforms have been found. Two highly related but distinctly processed pseudogenes that localize to chromosomes 1 and 13, respectively, have been reported. [provided by RefSeq, May 2011]
    Expression
    Ubiquitous expression in appendix (RPKM 7.7), lymph node (RPKM 7.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTPN2 in Genome Data Viewer
    Location:
    18p11.21
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (12785478..12884237, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (12948473..13046916, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (12785477..12884236, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene spire type actin nucleation factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:12701867-12702764 Neighboring gene proteasome assembly chaperone 2 Neighboring gene centrosomal protein 76 Neighboring gene NANOG hESC enhancer GRCh37_chr18:12722786-12723287 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:12734331-12734497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13105 Neighboring gene long intergenic non-protein coding RNA 1882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12766527-12767028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:12767029-12767528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12843102-12843610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12860375-12861038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12873719-12874330 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:12875558-12876170 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:12878042-12878251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9322 Neighboring gene eukaryotic translation initiation factor 4A2 pseudogene 1 Neighboring gene serine/threonine kinase 25 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions.
    EBI GWAS Catalog
    Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
    EBI GWAS Catalog
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
    EBI GWAS Catalog
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
    EBI GWAS Catalog
    Multiple common variants for celiac disease influencing immune gene expression.
    EBI GWAS Catalog
    Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
    EBI GWAS Catalog
    Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables STAT family protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables integrin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables non-membrane spanning protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine phosphatase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein tyrosine phosphatase activity TAS
    Traceable Author Statement
    more info
     
    enables receptor tyrosine kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables syntaxin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in B cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in erythrocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glucose homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in insulin receptor recycling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in insulin receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of ERK1 and ERK2 cascade IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of ERK1 and ERK2 cascade ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of T cell receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of epidermal growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of insulin receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of interleukin-2-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-4-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of interleukin-4-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-6-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of interleukin-6-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of lipid storage ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of macrophage colony-stimulating factor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of macrophage differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of platelet-derived growth factor receptor-beta signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of positive thymic T cell selection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of protein tyrosine kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of receptor signaling pathway via JAK-STAT IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of tumor necrosis factor-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of type I interferon-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in negative regulation of type II interferon-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of type II interferon-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of type II interferon-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of tyrosine phosphorylation of STAT protein IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in peptidyl-tyrosine dephosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of PERK-mediated unfolded protein response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of gluconeogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of hepatocyte growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of type II interferon-mediated signaling pathway TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome lumen IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    tyrosine-protein phosphatase non-receptor type 2
    Names
    T-cell protein tyrosine phosphatase
    NP_001193942.1
    NP_001295216.1
    NP_002819.2
    NP_536347.1
    NP_536348.1
    XP_016881373.1
    XP_024306996.1
    XP_024306997.2
    XP_047293651.1
    XP_047293652.1
    XP_047293653.1
    XP_054174875.1
    XP_054174876.1
    XP_054174877.1
    XP_054174878.1
    XP_054174879.1
    XP_054174880.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029116.1 RefSeqGene

      Range
      5099..97184
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001207013.2NP_001193942.1  tyrosine-protein phosphatase non-receptor type 2 isoform 4

      See identical proteins and their annotated locations for NP_001193942.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an additional in-frame exon in the middle coding region and an alternate 3' region, which includes a part of the C-terminal coding region, when compared to variant 1. The resulting isoform (4) has an additional internal segment and a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AK225706, BG699440, BQ010946
      Consensus CDS
      CCDS59306.1
      UniProtKB/Swiss-Prot
      P17706
      Related
      ENSP00000466936.1, ENST00000591115.5
      Conserved Domains (1) summary
      cl28904
      Location:19295
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily
    2. NM_001308287.1NP_001295216.1  tyrosine-protein phosphatase non-receptor type 2 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation from an alternate start codon compared to variant 1. The resulting isoform (5) has a shorter and distinct N-terminus, as compared to isoform 1.
      Source sequence(s)
      AB209569, AP001077
      Consensus CDS
      CCDS77155.1
      UniProtKB/TrEMBL
      K7EQG9, Q59F91
      Related
      ENSP00000467823.1, ENST00000591497.5
      Conserved Domains (2) summary
      cd00047
      Location:26245
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
      pfam00102
      Location:26245
      Y_phosphatase; Protein-tyrosine phosphatase
    3. NM_002828.4NP_002819.2  tyrosine-protein phosphatase non-receptor type 2 isoform 1

      See identical proteins and their annotated locations for NP_002819.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB209569, AK292570, AP001077, BG699440, DB350067
      Consensus CDS
      CCDS11865.1
      UniProtKB/Swiss-Prot
      A8K955, A8MXU3, K7ENG3, P17706, Q96AU5, Q96HR2
      UniProtKB/TrEMBL
      Q59F91
      Related
      ENSP00000311857.3, ENST00000309660.10
      Conserved Domains (1) summary
      cd14607
      Location:19272
      PTPc-N2; catalytic domain of tyrosine-protein phosphatase non-receptor type 2
    4. NM_080422.3NP_536347.1  tyrosine-protein phosphatase non-receptor type 2 isoform 2

      See identical proteins and their annotated locations for NP_536347.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 3' region, which includes a part of the C-terminal coding region, when compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AK290649, BG699440, BQ010946
      Consensus CDS
      CCDS11863.1
      UniProtKB/TrEMBL
      A8K3N4, Q59F91
      Related
      ENSP00000320298.3, ENST00000327283.7
      Conserved Domains (1) summary
      cd14607
      Location:19272
      PTPc-N2; catalytic domain of tyrosine-protein phosphatase non-receptor type 2
    5. NM_080423.3NP_536348.1  tyrosine-protein phosphatase non-receptor type 2 isoform 3

      See identical proteins and their annotated locations for NP_536348.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 3' region, which includes a part of the C-terminal coding region, when compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      BC016727, BQ010946
      Consensus CDS
      CCDS11864.1
      UniProtKB/Swiss-Prot
      P17706
      Related
      ENSP00000320546.3, ENST00000353319.8
      Conserved Domains (2) summary
      smart00194
      Location:5274
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:45274
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      12785478..12884237 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451228.2XP_024306996.1  tyrosine-protein phosphatase non-receptor type 2 isoform X6

      Conserved Domains (1) summary
      pfam00102
      Location:42229
      Y_phosphatase; Protein-tyrosine phosphatase
    2. XM_017025884.2XP_016881373.1  tyrosine-protein phosphatase non-receptor type 2 isoform X4

      UniProtKB/TrEMBL
      Q59F91
    3. XM_024451229.2XP_024306997.2  tyrosine-protein phosphatase non-receptor type 2 isoform X3

    4. XM_047437695.1XP_047293651.1  tyrosine-protein phosphatase non-receptor type 2 isoform X1

    5. XM_047437696.1XP_047293652.1  tyrosine-protein phosphatase non-receptor type 2 isoform X2

    6. XM_047437697.1XP_047293653.1  tyrosine-protein phosphatase non-receptor type 2 isoform X5

      UniProtKB/TrEMBL
      Q59F91

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      12948473..13046916 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318905.1XP_054174880.1  tyrosine-protein phosphatase non-receptor type 2 isoform X6

    2. XM_054318903.1XP_054174878.1  tyrosine-protein phosphatase non-receptor type 2 isoform X4

      UniProtKB/TrEMBL
      Q59F91
    3. XM_054318902.1XP_054174877.1  tyrosine-protein phosphatase non-receptor type 2 isoform X3

    4. XM_054318900.1XP_054174875.1  tyrosine-protein phosphatase non-receptor type 2 isoform X1

    5. XM_054318901.1XP_054174876.1  tyrosine-protein phosphatase non-receptor type 2 isoform X2

    6. XM_054318904.1XP_054174879.1  tyrosine-protein phosphatase non-receptor type 2 isoform X5

      UniProtKB/TrEMBL
      Q59F91