Abstract A missense risk variant (R620W) in the tyrosine phosphatase PTPN22 is strongly associated with multiple autoimmune diseases. To model this variant in vivo, we generated knock-in mice expressing the analogous variant (R619W) in murine Ptpn22. Expression of the variant significantly altered lymphocyte function and led to the development of systemic autoimmunity. Further, B lineage-restricted variant expression was sufficient to promote autoimmunity (Dai et al. JCI 2013). In the current study, we performed a detailed assessment of the impact of the variant on B cell tolerance, including its impact on the establishment of the naive repertoire. Utilizing a bone marrow (BM) chimera model, variant expressing B cells exhibited a competitive advantage over wild-type (WT) cells at multiple checkpoints, beginning in the BM and continuing in the periphery. Interestingly, while follicular (FM) B cells maintain this competitive advantage, marginal zone (MZ) B cells do not. In addition, using single cell BCR cloning, we observed a similar differential phenotype, where FM B cells are highly enriched for self-reactivity, while MZ B cells are less autoreactive than WT controls. Using a range of analyses to assess cell signaling, surface receptor expression, cell cycle and gene expression, we provide evidence that the risk variant regulates a complex interplay between the BCR and CD40 co-receptor pathways, culminating in a uniquely autoreactive pre-GC repertoire with important implications for subsequent development of autoimmunity.