IgA nephropathy (IgAN) is a major cause of kidney failure worldwide. Here we investigated the contribution of genome-wide protein coding variants to IgAN risk by performing a three-stage exome chip-based association study in 8,529 IgAN patients and 23,224 healthy controls of Han Chinese ancestry. We discovered a novel rare nonsynonymous risk variant in VEGFA, and further sequencing of VEGFA revealed twice as many carriers of other rare variants in 2,148 IgAN cases compared to 2,732 controls. We also discovered a common nonsynonymous risk variant in PKD1L3, and the variant was shown to be associated with nearby HP gene expression and lower protein level by previous and current studies. However, a common loss-of-function mutation of PKD1L3 did not show any association, suggesting that HP is more likely to be a susceptibility gene for IgAN. Our discovery of VEGFA and HP has expanded understanding on the genetic basis of IgAN susceptibility.