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

Gene ID: 5771, updated on 9-Dec-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
  • 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 histone H2AXY142 phosphatase activity 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 protein tyrosine phosphatase activity, metal-dependent IEA
Inferred from Electronic Annotation
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 chromatin remodeling IEA
Inferred from Electronic Annotation
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 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