Protein tyrosine phosphatase non-receptor 22 (PTPN22), a gene found on chromosome 1p13, which encodes lymphoid protein tyrosine phosphatase (LYP) was found to be associated with susceptibility to type 1 diabetes in 2004. Protein tyrosine phosphatases such as LYP are responsible for preventing spontaneous T cell activation and they have the ability to prevent the response to antigen by dephosphorylating and inactivating T cell receptors. A single nucleotide polymorphism (SNP) in the PTPN22 gene can lead to susceptibility to autoimmune diseases such as type 1 diabetes because of a decrease in negative regulation of hyper-reactive T cells. The first complete resequencing of the human PTPN22 gene was carried out in 2005. This sequence was further analysed for polymorphisms associated with type 1 diabetes and a SNP at 1858bp in codon 620 was found. Two alleles referred to as 1858C and 1858T were identified and the 1858T variant was shown to occur more often in type 1 diabetes populations: 30.6% of people with type 1 diabetes compared with 21.3% healthy controls are heterozygous for the polymorphism p = 0.0006.
LYP is expressed in other cells in addition to T cells including natural killer (NK) cells, B cells, macrophages and dendritic cells (DCs), and so could very well also have an effect on the function of several immune cells.