Causes. IgA nephropathy is caused by a buildup of the IgA protein in the kidneys. IgA proteins help the body fight infections. There are more of these proteins when you have an infection like the cold or flu.The protein buildup can damage the filters of the kidneys.auses. IgA nephropathy is caused by a buildup of the IgA protein in the kidneys. IgA proteins help the body fight infections. There are more of these proteins when you have an infection like the cold or flu.