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    PTPN22 protein tyrosine phosphatase non-receptor type 22 [ Homo sapiens (human) ]

    Gene ID: 26191, updated on 3-Dec-2024

    Summary

    Official Symbol
    PTPN22provided by HGNC
    Official Full Name
    protein tyrosine phosphatase non-receptor type 22provided by HGNC
    Primary source
    HGNC:HGNC:9652
    See related
    Ensembl:ENSG00000134242 MIM:600716; AllianceGenome:HGNC:9652
    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
    LYP; PEP; LYP1; LYP2; PTPN8; PTPN22.5; PTPN22.6
    Summary
    This gene encodes of member of the non-receptor class 4 subfamily of the protein-tyrosine phosphatase family. The encoded protein is a lymphoid-specific intracellular phosphatase that associates with the molecular adapter protein CBL and may be involved in regulating CBL function in the T-cell receptor signaling pathway. Mutations in this gene may be associated with a range of autoimmune disorders including Type 1 Diabetes, rheumatoid arthritis, systemic lupus erythematosus and Graves' disease. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Mar 2009]
    Expression
    Biased expression in bone marrow (RPKM 9.6), lymph node (RPKM 7.9) and 13 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTPN22 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113813811..113871759, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113825481..113883420, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114356433..114414334, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S2 pseudogene 14 Neighboring gene putative homeodomain transcription factor 1 Neighboring gene Sharpr-MPRA regulatory region 5734 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:114295082-114295283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114299147-114299702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114301981-114302560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1216 Neighboring gene round spermatid basic protein 1 Neighboring gene Sharpr-MPRA regulatory region 4295 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114353909-114354438 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr1:114354439-114354968 and GRCh37_chr1:114354969-114355498 Neighboring gene AP4B1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1538 Neighboring gene BCL2 like 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1540 Neighboring gene adaptor related protein complex 4 subunit beta 1 Neighboring gene DNA cross-link repair 1B

    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

    Associated conditions

    Description Tests
    Diabetes mellitus type 1
    MedGen: C0011854 OMIM: 222100 GeneReviews: Not available
    Compare labs
    Rheumatoid arthritis
    MedGen: C0003873 OMIM: 180300 GeneReviews: Not available
    Compare labs
    Systemic lupus erythematosus
    MedGen: C0024141 OMIM: 152700 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene.
    EBI GWAS Catalog
    A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis.
    EBI GWAS Catalog
    Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    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 meta-analysis identifies seven new rheumatoid arthritis risk loci.
    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
    Identification of novel genetic Loci associated with thyroid peroxidase antibodies and clinical thyroid disease.
    EBI GWAS Catalog
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
    EBI GWAS Catalog
    Novel associations for hypothyroidism include known autoimmune risk loci.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Novel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide association study.
    EBI GWAS Catalog
    REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis.
    EBI GWAS Catalog
    Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08.
    EBI GWAS Catalog
    Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
    EBI GWAS Catalog
    TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study.
    EBI GWAS Catalog
    Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
    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 SH3 domain binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H2AXY142 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables kinase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables non-membrane spanning protein tyrosine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    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 ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in T cell receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in T cell receptor signaling pathway TAS
    Traceable Author Statement
    more info
     
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to muramyl dipeptide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipopolysaccharide-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of JUN kinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of T cell activation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-6 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of interleukin-8 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of p38MAPK cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of tumor necrosis factor production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phosphoanandamide dephosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of NLRP3 inflammasome complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein K63-linked ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of toll-like receptor 3 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of toll-like receptor 4 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of type I interferon production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of type II interferon production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein dephosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein dephosphorylation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of B cell receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of innate immune response IC
    Inferred by Curator
    more info
    PubMed 
    involved_in regulation of natural killer cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of non-canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of non-canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to lipopolysaccharide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol 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 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    tyrosine-protein phosphatase non-receptor type 22
    Names
    PEST-domain phosphatase
    hematopoietic cell protein-tyrosine phosphatase 70Z-PEP
    lymphoid-specific protein tyrosine phosphatase
    protein tyrosine phosphatase, non-receptor type 22 (lymphoid)
    protein tyrosine phosphatase, non-receptor type 8
    NP_001180360.2
    NP_001295226.2
    NP_036543.5
    NP_057051.4
    XP_011539523.1
    XP_011539524.1
    XP_011539525.1
    XP_011539527.1
    XP_016856494.1
    XP_016856495.1
    XP_047273586.1
    XP_047273587.1
    XP_047273588.1
    XP_054191914.1
    XP_054191915.1
    XP_054191916.1
    XP_054191917.1
    XP_054191918.1
    XP_054191919.1
    XP_054191920.1
    XP_054191921.1
    XP_054191922.1

    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_011432.2 RefSeqGene

      Range
      5047..62948
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193431.3NP_001180360.2  tyrosine-protein phosphatase non-receptor type 22 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AL137856
      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
    2. NM_001308297.2NP_001295226.2  tyrosine-protein phosphatase non-receptor type 22 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      AL137856
      Consensus CDS
      CCDS76191.1
      UniProtKB/TrEMBL
      F5H2S8, G3K0T4
      Related
      ENSP00000439372.2, ENST00000538253.5
    3. NM_012411.6NP_036543.5  tyrosine-protein phosphatase non-receptor type 22 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AL137856
      Consensus CDS
      CCDS864.2
      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
      UniProtKB/TrEMBL
      A0A0A0MTE6
      Related
      ENSP00000435176.1, ENST00000528414.5
    4. NM_015967.8NP_057051.4  tyrosine-protein phosphatase non-receptor type 22 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA836401, AF001846, AF077031, AL137856, BC071670, DB145424
      Consensus CDS
      CCDS863.1
      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
      UniProtKB/TrEMBL
      A0A0B4J1S7
      Related
      ENSP00000352833.5, ENST00000359785.10

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      113813811..113871759 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417630.1XP_047273586.1  tyrosine-protein phosphatase non-receptor type 22 isoform X3

      UniProtKB/TrEMBL
      G3K0T4
    2. XM_047417631.1XP_047273587.1  tyrosine-protein phosphatase non-receptor type 22 isoform X4

      UniProtKB/TrEMBL
      G3K0T4
    3. XM_011541225.3XP_011539527.1  tyrosine-protein phosphatase non-receptor type 22 isoform X9

      UniProtKB/TrEMBL
      G3K0T4
      Conserved Domains (2) summary
      smart00194
      Location:24264
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:56264
      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 ...
    4. XM_047417632.1XP_047273588.1  tyrosine-protein phosphatase non-receptor type 22 isoform X5

      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
    5. XM_011541221.2XP_011539523.1  tyrosine-protein phosphatase non-receptor type 22 isoform X1

      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
      Conserved Domains (2) summary
      smart00194
      Location:24262
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:56262
      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 ...
    6. XM_011541222.2XP_011539524.1  tyrosine-protein phosphatase non-receptor type 22 isoform X2

      UniProtKB/TrEMBL
      E9PMT0
      Conserved Domains (2) summary
      smart00194
      Location:24288
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:56288
      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 ...
    7. XM_017001005.3XP_016856494.1  tyrosine-protein phosphatase non-receptor type 22 isoform X7

      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
    8. XM_011541223.3XP_011539525.1  tyrosine-protein phosphatase non-receptor type 22 isoform X6

      UniProtKB/TrEMBL
      E9PMT0
      Conserved Domains (2) summary
      smart00194
      Location:24288
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:56288
      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 ...
    9. XM_017001006.2XP_016856495.1  tyrosine-protein phosphatase non-receptor type 22 isoform X8

      Conserved Domains (1) summary
      cd14602
      Location:57290
      PTPc-N22; catalytic domain of tyrosine-protein phosphatase non-receptor type 22

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      113825481..113883420 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335941.1XP_054191916.1  tyrosine-protein phosphatase non-receptor type 22 isoform X3

      UniProtKB/TrEMBL
      G3K0T4
    2. XM_054335942.1XP_054191917.1  tyrosine-protein phosphatase non-receptor type 22 isoform X4

      UniProtKB/TrEMBL
      G3K0T4
    3. XM_054335947.1XP_054191922.1  tyrosine-protein phosphatase non-receptor type 22 isoform X9

      UniProtKB/TrEMBL
      G3K0T4
    4. XM_054335943.1XP_054191918.1  tyrosine-protein phosphatase non-receptor type 22 isoform X5

      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
    5. XM_054335939.1XP_054191914.1  tyrosine-protein phosphatase non-receptor type 22 isoform X1

      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
    6. XM_054335940.1XP_054191915.1  tyrosine-protein phosphatase non-receptor type 22 isoform X2

      UniProtKB/TrEMBL
      E9PMT0
    7. XM_054335945.1XP_054191920.1  tyrosine-protein phosphatase non-receptor type 22 isoform X7

      UniProtKB/Swiss-Prot
      A0N0K6, B1ALC8, D4NZ71, E9PLD8, E9PPI1, O95063, O95064, Q6IPX8, Q8WVM1, Q9Y2R2
    8. XM_054335944.1XP_054191919.1  tyrosine-protein phosphatase non-receptor type 22 isoform X6

      UniProtKB/TrEMBL
      E9PMT0
    9. XM_054335946.1XP_054191921.1  tyrosine-protein phosphatase non-receptor type 22 isoform X8