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

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: mouse all
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Genomic context

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_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene polymorphisms (rs2542151, rs7234029) in Egyptian Behcet's disease patients: a preliminary report.
Title: Protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene polymorphisms (rs2542151, rs7234029) in Egyptian Behçet's disease patients: a preliminary report.
A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis.
Title: A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis.
Haploinsufficiency in PTPN2 leads to early-onset systemic autoimmunity from Evans syndrome to lupus.
Title: Haploinsufficiency in PTPN2 leads to early-onset systemic autoimmunity from Evans syndrome to lupus.
PTPN2 inhibits the proliferation of psoriatic keratinocytes by dephosphorylation of STAT3.
Title: PTPN2 inhibits the proliferation of psoriatic keratinocytes by dephosphorylation of STAT3.
Stem-Cell-Derived beta-Like Cells with a Functional PTPN2 Knockout Display Increased Immunogenicity.
Title: Stem-Cell-Derived β-Like Cells with a Functional PTPN2 Knockout Display Increased Immunogenicity.
PTPN2 in the Immunity and Tumor Immunotherapy: A Concise Review.
Title: PTPN2 in the Immunity and Tumor Immunotherapy: A Concise Review.
The first association study of Protein Tyrosine Phosphatase, Non-Receptor Type 2 (PTPN2) gene polymorphisms in Malaysian patients with Crohn's disease.
Title: The first association study of Protein Tyrosine Phosphatase, Non-Receptor Type 2 (PTPN2) gene polymorphisms in Malaysian patients with Crohn's disease.
Structural characterization of a pathogenic mutant of human protein tyrosine phosphatase PTPN2 (Cys216Gly) that causes very early onset autoimmune enteropathy.
Title: Structural characterization of a pathogenic mutant of human protein tyrosine phosphatase PTPN2 (Cys216Gly) that causes very early onset autoimmune enteropathy.
PTPN2 Regulates the Interferon Signaling and Endoplasmic Reticulum Stress Response in Pancreatic beta-Cells in Autoimmune Diabetes.
Title: PTPN2 Regulates the Interferon Signaling and Endoplasmic Reticulum Stress Response in Pancreatic β-Cells in Autoimmune Diabetes.
PTPN2 elicits cell autonomous and non-cell autonomous effects on antitumor immunity in triple-negative breast cancer.
Title: PTPN2 elicits cell autonomous and non-cell autonomous effects on antitumor immunity in triple-negative breast cancer.

Submit: New GeneRIF Correction See all GeneRIFs (129)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SGC31554 (e-PCR)
- UniSTS:76564

RH65175 (e-PCR)
- UniSTS:89633

sY3084 (e-PCR)
- UniSTS:515126

GDB:217060 (e-PCR)
- UniSTS:156225

STS-N53696 (e-PCR)
- UniSTS:76658

D1S1425 (e-PCR)
- UniSTS:149621

RH36905 (e-PCR)
- UniSTS:87932

RH12560 (e-PCR)
- UniSTS:84170

GDB:196599 (e-PCR)
- UniSTS:155871

ECD04345 (e-PCR)
- UniSTS:285422

STS-M78585 (e-PCR)
- UniSTS:42996

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

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Preferred Names: tyrosine-protein phosphatase non-receptor type 2

Names: T-cell protein tyrosine phosphatase

NP_001193942.1

EC 3.1.3.48

NP_001295216.1

EC 3.1.3.48

NP_002819.2

EC 3.1.3.48

NP_536347.1

EC 3.1.3.48

NP_536348.1

EC 3.1.3.48

XP_016881373.1

EC 3.1.3.48

XP_024306996.1

EC 3.1.3.48

XP_024306997.2

EC 3.1.3.48

XP_047293651.1

EC 3.1.3.48

XP_047293652.1

EC 3.1.3.48

XP_047293653.1

EC 3.1.3.48

XP_054174875.1

EC 3.1.3.48

XP_054174876.1

EC 3.1.3.48

XP_054174877.1

EC 3.1.3.48

XP_054174878.1

EC 3.1.3.48

XP_054174879.1

EC 3.1.3.48

XP_054174880.1

EC 3.1.3.48

NCBI Reference Sequences (RefSeq)

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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

NG_029116.1 RefSeqGene

Range

5099..97184

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001207013.2 → NP_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:19 → 295

PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily
NM_001308287.1 → NP_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:26 → 245

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:26 → 245

Y_phosphatase; Protein-tyrosine phosphatase
NM_002828.4 → NP_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:19 → 272

PTPc-N2; catalytic domain of tyrosine-protein phosphatase non-receptor type 2
NM_080422.3 → NP_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:19 → 272

PTPc-N2; catalytic domain of tyrosine-protein phosphatase non-receptor type 2
NM_080423.3 → NP_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:5 → 274

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:45 → 274

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

NC_000018.10 Reference GRCh38.p14 Primary Assembly

Range

12785478..12884237 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam00102
Location:42 → 229

Y_phosphatase; Protein-tyrosine phosphatase
XM_017025884.2 → XP_016881373.1 tyrosine-protein phosphatase non-receptor type 2 isoform X4

UniProtKB/TrEMBL

Q59F91
XM_024451229.2 → XP_024306997.2 tyrosine-protein phosphatase non-receptor type 2 isoform X3
XM_047437695.1 → XP_047293651.1 tyrosine-protein phosphatase non-receptor type 2 isoform X1
XM_047437696.1 → XP_047293652.1 tyrosine-protein phosphatase non-receptor type 2 isoform X2
XM_047437697.1 → XP_047293653.1 tyrosine-protein phosphatase non-receptor type 2 isoform X5

UniProtKB/TrEMBL

Q59F91

Alternate T2T-CHM13v2.0

Genomic

NC_060942.1 Alternate T2T-CHM13v2.0

Range

12948473..13046916 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054318905.1 → XP_054174880.1 tyrosine-protein phosphatase non-receptor type 2 isoform X6
XM_054318903.1 → XP_054174878.1 tyrosine-protein phosphatase non-receptor type 2 isoform X4

UniProtKB/TrEMBL

Q59F91
XM_054318902.1 → XP_054174877.1 tyrosine-protein phosphatase non-receptor type 2 isoform X3
XM_054318900.1 → XP_054174875.1 tyrosine-protein phosphatase non-receptor type 2 isoform X1
XM_054318901.1 → XP_054174876.1 tyrosine-protein phosphatase non-receptor type 2 isoform X2
XM_054318904.1 → XP_054174879.1 tyrosine-protein phosphatase non-receptor type 2 isoform X5

UniProtKB/TrEMBL

Q59F91