Egyptians did some fascinating stuff in the past; Built pyramids, were a prosperous and mighty nation, tried to keep the body of their dead in the best shape they could. Well there's another thing they could be accredited: a toe (of Toetankhamun ?) might give them the title of having the world's earliest functional prosthetic body part.
You'll have to admit it was something expected, since a nation that advanced had the wealth and the knowledge to attempt such an action. Genetic malformations are a natural phenomenon, since genes can be wrongly placed, replaced, removed or even drifted during cell division (hail to evolution). We've come a long way from apes to homo sapiens sapiens species. It could also be an amputation because of an infection gone worse, which of course could entitle the "Pharaoh" as defective and unable to run a kingdom without a toe (Hey, I'm just making this up! Sounds impossible, but everyone knows what religion and demagogy power can achieve).
More info here.