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

Gene ID: 26191, updated on 6-Jul-2014
Official Symbol
PTPN22provided by HGNC
Official Full Name
protein tyrosine phosphatase, non-receptor type 22 (lymphoid)provided by HGNC
Primary source
HGNC:9652
See related
Ensembl:ENSG00000134242; HPRD:06100; MIM:600716; Vega:OTTHUMG00000011936
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
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]
See PTPN22 in Epigenomics, MapViewer
Location:
1p13.2
Exon count :
21
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 1 NC_000001.11 (113813811..113871753, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114356433..114414375, 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 round spermatid basic protein 1 Neighboring gene uncharacterized LOC101928822 Neighboring gene AP4B1 antisense RNA 1 Neighboring gene BCL2-like 15 Neighboring gene adaptor-related protein complex 4, beta 1 subunit

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

NHGRI GWAS Catalog

Description
A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene.
NHGRI GWA Catalog
A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis.
NHGRI GWA Catalog
Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
NHGRI GWA Catalog
Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
NHGRI GWA Catalog
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
NHGRI GWA Catalog
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
NHGRI GWA Catalog
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
NHGRI GWA Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
NHGRI GWA Catalog
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci.
NHGRI GWA Catalog
Novel associations for hypothyroidism include known autoimmune risk loci.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Novel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide association study.
NHGRI GWA Catalog
REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis.
NHGRI GWA Catalog
Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08.
NHGRI GWA Catalog
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
NHGRI GWA Catalog
TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study.
NHGRI GWA Catalog
Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
NHGRI GWA Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SH3 domain binding ISS
Inferred from Sequence or Structural Similarity
more info
 
kinase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of T cell activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of T cell receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-tyrosine dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-tyrosine dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
phosphoanandamide dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
protein dephosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
protein dephosphorylation TAS
Traceable Author Statement
more info
 
regulation of B cell receptor signaling pathway NAS
Non-traceable Author Statement
more info
PubMed 
regulation of innate immune response IC
Inferred by Curator
more info
 
regulation of natural killer cell proliferation IDA
Inferred from Direct Assay
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
 
cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
tyrosine-protein phosphatase non-receptor type 22
Names
tyrosine-protein phosphatase non-receptor type 22
lymphoid phosphatase
PEST-domain phosphatase
lymphoid-specific protein tyrosine phosphatase
protein tyrosine phosphatase, non-receptor type 8
hematopoietic cell protein-tyrosine phosphatase 70Z-PEP
NP_001180360.1
NP_036543.4
NP_057051.3

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_011432.1 

    Range
    5001..62943
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001193431.1NP_001180360.1  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)
    AA836401, AK303124, AL137856, DB145424, GU479452
    UniProtKB/TrEMBL
    B4DZW8
    UniProtKB/Swiss-Prot
    Q9Y2R2
    Conserved Domains (2) summary
    smart00194
    Location:24288
    Blast Score: 906
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:56288
    Blast Score: 889
    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 ...
  2. NM_012411.4NP_036543.4  tyrosine-protein phosphatase non-receptor type 22 isoform 2

    See proteins identical to NP_036543.4

    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)
    AA836401, AL137856, BC071670, DB145424
    Consensus CDS
    CCDS864.2
    UniProtKB/Swiss-Prot
    Q9Y2R2
    Related
    ENSP00000435176, OTTHUMP00000013721, ENST00000528414, OTTHUMT00000033018
    Conserved Domains (2) summary
    smart00194
    Location:24252
    Blast Score: 798
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:56252
    Blast Score: 781
    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 ...
  3. NM_015967.5NP_057051.3  tyrosine-protein phosphatase non-receptor type 22 isoform 1

    See proteins identical to NP_057051.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA836401, AF077031, AK303124, AL137856, DB145424
    Consensus CDS
    CCDS863.1
    UniProtKB/TrEMBL
    B4DZW8
    UniProtKB/Swiss-Prot
    Q9Y2R2
    Related
    ENSP00000352833, OTTHUMP00000013720, ENST00000359785, OTTHUMT00000033015
    Conserved Domains (2) summary
    smart00194
    Location:24288
    Blast Score: 907
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:56288
    Blast Score: 890
    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: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

    Range
    113813811..113871753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005270738.1XP_005270795.1  

    Conserved Domains (2) summary
    smart00194
    Location:24264
    Blast Score: 800
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:56264
    Blast Score: 784
    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 ...

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    112214556..112272493
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

    Range
    114471278..114529225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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