Selection has not yet been examined in a controlled genetic environment. Yeh et al. recently reported that overexpression of wild type Pep under control of the distal Lck promoter did not result in alteration of thymocyte numbers in the NOD background, however the distal Lck promoter is expressed only in late stages of thymocyte selection, and the effect of the autoimmune-predisposing R620W variant was not assessed. In this study, we addressed effects of the human LYP-W620 variant on thymocyte signaling and selection by expressing the variant phosphatase under control of the proximal Lck promoter. To model effects of altered enzymatic activity inherent in LYPW620, we studied mice exhibiting low overexpression levels of the active human phosphatase in thymocytes. To detect possible effects unrelated to the increased phosphatase activity, we also examined animals overexpressing an enzymatically-inactive mutant of the LYP-W620 phosphatase. Mice transgenic for the active phosphatase displayed reduced thymocyte TCR signaling when compared to mice transgenic for the inactive phosphatase or to non transgenic Diacerein littermates. However no significant alterations of T cell selection or of thymic Treg output were observed in LYP-W620 transgenic mice. Our study suggests that the reported gain-of-function activity of LYP-W620 is insufficient to significantly alter thymic output; thus it is unlikely that its major Ginsenoside-F5 disease-predisposing role is exerted during thymocyte selection. With respect to genetic effect potency, the LYP-R620W polymorphism currently ranks in second and third position, respectively, as a risk factor for RA and for type 1 diabetes. Although it is evident that the R620W variation is one of the major non-HLA genetic risk factors for autoimmunity, its mechanism of action at the molecular level and its role in the immunopathogenesis of disease remain unclear. Our experiments in primary T cells from type 1 diabetes subjects and in Jurkat and primary human T cells overexpressing LYPW lead us to propose a model that LYP-W620 acts as a gainof-function variant in phosphatase activity and in negative regulation of TCR signaling. Accordingly, an initial hypothesis as to how the R620W variation might promote autoimmunity was that variant LYP augments inhibition of thymocyte TCR signaling and allows the escape of higher numbers of auto-reactive T cells or of T cells exhibiting a higher functional avidity. Since formulation of the hypothesis, additional data variably supporting a “gain-of-function”, “loss-of-function” or “altered-function” phenotype of LYP-W620 in TCR signaling have been published. Ptpn22-deficient mice exhibit abnormal accumulation of effector-like and memory T cells and heightened lymphoproliferation capacity without clear-cut breaches in peripheral tolerance, but it has remained unclear whether these phenotypes solely relied on a lack of peripheral or thymic Pep expression. Two independent studies have found evidence of increased qualitative positive thymocyte selection in Ptpn22 KO mice transgenic for the D011.10 and OT-II TCRs. Another group recently overexpressed WT Pep under control of the T lineage specific distal Lck promoter, and found no alterations in thymocyte subpopulation numbers in transgenic vs non transgenic mice. However, based on the published Ptpn22 KO, knock-in, or overexpression studies, no prediction could be made how a presumed gain of function R620W variant of human LYP might impact negative selection of auto-reactive T cells. Our study was designed to test the hypothesis that the gain-of-function inhibition of TCR signaling by LYP-W620 in thymocytes is sufficient to alter thymic output in a manner that could increase predisposition to autoimmunity.