Kira is a coordinator. Basically, a coordinator is a human who was genetically enhanced to be smarter, less prone to disease, and generally better off than naturals (humans born naturally). There is a good summary of the history of coordinators here. Kira is a first-generation coordinator, meaning his parents are naturals.
However, in one episode of the first series it shows Kira's friends on Archangel visiting their parents in Orb. Kira elects not to see his for various reasons, but it does show them. We learn in episode 45 that those were not his real parents.
In this episode, Klueze lures Mwu and Kira into an abandoned laboratory on the Mendel colony (likely a reference to scientist Gregor Mendel, who is said to have been "the father of genetics"). He then begins to manipulate Kira by telling him he was one of the creations of a man named Dr. Hibiki, and the only one who survived. They were all vain attempts to create the "ultimate coordinator", but they all died, leaving Kira as the only successful try. Klueze calls him "the dream of mankind", and this explains how he's able to pilot so well amongst other things. Not much more is revealed about his being the ultimate coordinator.