Human Gene PTPN22 (uc001edt.3)
  Description: Homo sapiens protein tyrosine phosphatase, non-receptor type 22 (lymphoid) (PTPN22), transcript variant 2, mRNA.
RefSeq Summary (NM_012411): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:114,356,433-114,414,375 Size: 57,943 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:114,362,205-114,414,245 Size: 52,041 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:114,356,433-114,414,375)mRNA (may differ from genome)Protein (179 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIPubMedReactome
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-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PTPN22
CDC HuGE Published Literature: PTPN22
Positive Disease Associations: alopecia areata , Arthritis, Rheumatoid , asthma rheumatoid arthritis , Autoimmune Diseases|Lupus Erythematosus, Systemic|Systemic lupus erythematosus , Autoimmune Diseases|Vitiligo , Bacterial Infections|Postoperative Complications , Crohn Disease , Crohn's disease , Diabetes Mellitus, Type 1 , diabetes, type 1 , diabetes, type 1 juvenile arthritis , diabetes, type 2 rheumatoid arthritis , Graves' disease , Juvenile Idiopathic arthritis , lupus , lupus erythematosus , lupus erythematosus; rheumatoid arthritis , lupus erythematosus; rheumatoid arthritis; cholangitis, sclerosing; celiac disease; juvenile arthrit , myasthenia gravis , Myositis , psoriatic arthritis , rheumatoid arthritis , rheumatoid arthritis thyroid disease, autoimmune , rheumatoid arthritis; juvenile arthritis , sclerosis, systemic , systemic lupus erythematosus , type 1 diabetes , Vitiligo
Related Studies:
  1. alopecia areata
    Kemp, E. H. et al. 2006, The Non-Synonymous C1858T Substitution in the PTPN22 Gene is Associated with Susceptibility to the Severe Forms of Alopecia Areata, Hum Immunol 2006 67(7) 535-9. [PubMed 16829308]
  2. Arthritis, Rheumatoid
    Karen H Costenbader , et al. Arthritis research & therapy 2008 10(3):R52, Genetic polymorphisms in PTPN22, PADI-4, and CTLA-4 and risk for rheumatoid arthritis in two longitudinal cohort studies: evidence of gene-environment interactions with heavy cigarette smoking., Arthritis research & therapy 2008 10(3):R52. [PubMed 18462498]
    After adjusting for smoking and reproductive factors, PTPN22 was associated with RA risk among Caucasian women in these cohorts.We found both additive and multiplicative interactions between PTPN22 and heavy cigarette smoking.
  3. Arthritis, Rheumatoid
    Robert M Plenge et al. The New England journal of medicine 2007, TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study., The New England journal of medicine. [PubMed 17804836]
    A common genetic variant at the TRAF1-C5 locus on chromosome 9 is associated with an increased risk of anti-CCP-positive rheumatoid arthritis.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PTPN22
Diseases sorted by gene-association score: systemic lupus erythematosus* (916), rheumatoid arthritis* (667), diabetes mellitus, insulin-dependent* (635), vitiligo-associated multiple autoimmune disease susceptibility 6* (300), vogt-koyanagi-harada disease* (47), arthritis (31), lupus erythematosus (25), graves' disease (18), rheumatoid factor-negative juvenile idiopathic arthritis* (18), pediatric systemic lupus erythematosus* (18), temporal arteritis* (17), wegener granulomatosis* (15), addison's disease (14), hashimoto thyroiditis (13), palindromic rheumatism (11), hypersensitivity reaction type ii disease (11), vitiligo-associated multiple autoimmune disease susceptibility 1 (10), anterior uveitis (9), alpha/beta t-cell lymphopenia with gamma/delta t-cell expansion, severe cytomegalovirus infection, and autoimmunity (9), psoriatic arthritis (9), oligoarticular juvenile idiopathic arthritis* (8), celiac disease (8), alopecia areata (8), autoimmune addison disease (7), multifocal motor neuropathy (7), sapho syndrome (7), autoimmune disease of endocrine system (6), adrenal cortical hypofunction (5), rheumatoid arthritis, systemic juvenile (1), bone inflammation disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.14 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 67.21 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.30130-0.233 Picture PostScript Text
3' UTR -234.701165-0.201 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00102 - Protein-tyrosine phosphatase

SCOP Domains:
52799 - (Phosphotyrosine protein) phosphatases II

ModBase Predicted Comparative 3D Structure on Q9Y2R2-5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  KJ902426 - Synthetic construct Homo sapiens clone ccsbBroadEn_11820 PTPN22 gene, encodes complete protein.
BC071670 - Homo sapiens protein tyrosine phosphatase, non-receptor type 22 (lymphoid), mRNA (cDNA clone MGC:87871 IMAGE:5497108), complete cds.
BC017785 - Homo sapiens protein tyrosine phosphatase, non-receptor type 22 (lymphoid), mRNA (cDNA clone IMAGE:4666653), complete cds.
AF001846 - Homo sapiens lymphoid phosphatase LyP1 mRNA, complete cds.
JD305076 - Sequence 286100 from Patent EP1572962.
JD355263 - Sequence 336287 from Patent EP1572962.
JD545300 - Sequence 526324 from Patent EP1572962.
AF150732 - Homo sapiens protein tyrosine phosphatase (PTP) mRNA, complete cds.
AF077031 - Homo sapiens protein tyrosine phosphatase homolog mRNA, complete cds.
AK303124 - Homo sapiens cDNA FLJ55436 complete cds, highly similar to Tyrosine-protein phosphatase non-receptortype 22 (EC 3.1.3.48).
JD538574 - Sequence 519598 from Patent EP1572962.
GU479452 - Homo sapiens tyrosine phosphatase LYP variant 3 mRNA, complete cds, alternatively spliced.
JN084012 - Homo sapiens tyrosine-protein phosphatase non-receptor type 22 isoform 8 (PTPN22) mRNA, complete cds, alternatively spliced.
AB587398 - Synthetic construct DNA, clone: pF1KB5747, Homo sapiens PTPN22 gene for protein tyrosine phosphatase, non-receptor type 22, without stop codon, in Flexi system.
AK310698 - Homo sapiens cDNA, FLJ17740.
AK310570 - Homo sapiens cDNA, FLJ17612.
AF001847 - Homo sapiens lymphoid phosphatase LyP2 mRNA, complete cds.
U69700 - Human protein tyrosine phosphatase PEP mRNA, partial cds.
JD053341 - Sequence 34365 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y2R2 (Reactome details) participates in the following event(s):

R-HSA-8855375 PTPN22 dissociates from CSK
R-HSA-8852200 Inactivation of LCK by PTPN22
R-HSA-8855381 PTPN22 dephosphorylates ZAP70
R-HSA-202427 Phosphorylation of CD3 and TCR zeta chains
R-HSA-202403 TCR signaling
R-HSA-202430 Translocation of ZAP-70 to Immunological synapse
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: BC017785, PTPN8, Q9Y2R2-5
UCSC ID: uc001edt.3
RefSeq Accession: NM_012411
Protein: Q9Y2R2-5, splice isoform of Q9Y2R2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC017785.1
exon count: 8CDS single in 3' UTR: no RNA size: 1817
ORF size: 540CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 1171.00frame shift in genome: no % Coverage: 98.29
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.