Large-scale DNA sequencing identifies rare variants associated with Systemic Lupus Erythematosus susceptibility in known risk genes

•Common genetic variants often have a modest effect on the SLE risk.•Rare variants in genes associated to SLE could have an effect on susceptibility.•Genomic DNA of 200 SLE patients was sequenced by whole exome sequencing.•19 rare variants were identified in TNFAIP3, TRAF3IP2, STAT4 and HCP5 genes.•Rare variants associated to SLE could help to understand its pathogenic mechanisms. The identification of rare genetic variants associated to Systemic Lupus Erythematosus (SLE) could also help to understand the pathogenic mechanisms at the basis of the disease. In this study we have analyzed a cohort of 200 Italian SLE patients in order to explore the rare protein-coding variants in five genes (TNFAIP3, STAT4, IL10, TRAF3IP2, and HCP5) already investigated for commons variants found associated in our previous studies. Genomic DNA of 200 SLE patients was sequenced by whole exome sequencing. The identified variants were filtered by frequency and evaluated by in silico predictions. Allelic association analysis was performed with standard Fisher’s exact test. Introducing a cutoff at MAF