RVT comparing the distribution of rare variants of sJIA cases with that of the ExAC NFE population revealed significant rare variant associations between sJIA and LYST, STXBP2, UNC13D and MEFV. We also discovered recurrent mutations of STXBP2, UNC13D, and MEFV among the sJIA cohort that were not observed in the ExAC population. Here, UNC13D is linked to systemic-onset juvenile idiopathic arthritis.