Signaling lymphocyte activation molecules (SLAMs) play an integral role in immune regulation. Polymorphisms in the SLAM family receptors are implicated in human and mouse model of lupus disease. The lupus-associated, somatically mutated and class-switched pathogenic autoantibodies are generated in spontaneously developed germinal centers (Spt-GCs) in secondary lymphoid organs. The role and mechanism of B cell-intrinsic expression of polymorphic SLAM receptors that affect B cell tolerance at the GC checkpoint is not clear. Here, we generated several bacterial artificial chromosome (BAC) transgenic mice that overexpress B6 alleles of different SLAM family genes in autoimmune-prone B6.Sle1b mice. B6.Sle1b mice overexpressing B6-derived Ly108 and CD84 exhibit a significant reduction in the Spt-GC response and autoantibody production compared to B6.Sle1b mice. These data suggest a prominent role of Sle1b-derived Ly108 and CD84 in altering the GC checkpoint. We further confirm that expression of lupus-associated CD84 and Ly108 specifically on GC B cells in B6.Sle1b mice is sufficient to break B cell tolerance leading to an increase in autoantibody production. In addition, we observe that B6.Sle1b B cells have reduced BCR signaling, and a lower frequency of B cell-T cell conjugates, which are reversed in B6.Sle1b mice overexpressing B6 alleles of CD84 and Ly108. Finally, we find a significant decrease in apoptotic GC B cells in B6.Sle1b mice compared to B6 controls. Our study establishes the central role of GC B cell-specific CD84 and Ly108 expression in maintaining B cell tolerance in GCs and in preventing autoimmunity.