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Using long-read single molecule real-time sequencing (SMRT), we detected the breakpoints of three SVs. The identified SVs included 1) a deletion of the entire CFH in one patient with IC-MPGN; 2) an increased number of CFHR4 copies in one IC-MPGN and three C3G patients; 3) a deletion from CFHR3-intron 3 to CFHR3-3'UTR (CFHR34 - 6 Δ) that results in a FHR3-FHR1 hybrid protein in a C3G patient; and 4) a CFHR31 - 5-CFHR410 hybrid gene in a C3G patient. This work highlights the contribution of CFH-CFHR CNVs to the p