xx_tomorrowsashes_xx
I also lean towards mutation because mutated genes tend to degenerate rather quickly. Hence why Kakashi asks Itachi how his eyes have been/are, (Episode 12 of Shippuuden I believe). Kakashi's comment leads me to believe that the supposed mutated genes that give the Uchiha clan Sharingan will sooner or later (sooner with more use) cause the user to go blind altogether.
thats only when they use the.... what is it... the freaky genjutsu thing.....aha the Mangekyou Sharingan