In the background of depressed C3, thrombocytopenia, a history of accelerated hypertension, and early-onset chronic kidney disease in three generations, whole exome next-generation sequencing with in silico analysis was done that revealed homozygous deletion in the complement factor H-related 3 (CFHR3) gene [1(g.(196774945_196779161)_(196794074_196793316)del)]. This evidence concerns the gene CFHR3 and chronic kidney disease.