My rats foot is messed up!?

If he was born that way, I don't see any need to worry about it unless he seems to be in pain. If he is in pain, take him to the vet of course, they can tell you what the best course or action is. If he WAS born with it, he will adapt. He may be a bit clumsy, and lazy if he doesn't like walking on it, so put some hammocks in the cage if it has high levels so he doens't hurt himself if he falls.