This study has identified the trigenic inheritance of rare missense variants in PAK2 (c.128T > C, p. Val43Ala), TAP2 (c.1417G > A, p. Val473Ile), and PLCL1 (c.1403T > A, p. Phe468Tyr) genes as the molecular basis of polygenic autoimmune diseases CeD, AiT, SLE, and TIDM. Here, TAP2 is linked to cranioectodermal dysplasia.