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
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]
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.
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.
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.
SCOP Domains: 52799 - (Phosphotyrosine protein) phosphatases II
ModBase Predicted Comparative 3D Structure on Q9Y2R2-5
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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.
Mouse
Rat
Zebrafish
D. melanogaster
C. elegans
S. cerevisiae
No ortholog
No ortholog
No ortholog
No ortholog
No ortholog
No 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):