The rare variants we identified in the PAK2, TAP2, p. Val473Ile, and PLCL1 genes are postulated to contribute to the pathogenesis of CeD, AiT, SLE, and TIDM by modulating antigen processing and presentation, T cell receptor signaling, and immunodeficiency pathways. Here, SLC5A8 is linked to systemic lupus erythematosus.