Thanks everyone! Joshie, I don't know about the stud because he wasn't ours but the mare had genetic testing and the deformity didn't come from her. She has had two more babies since with different studs and they are all fine.
I'm hoping I can convince them to send him to a therapeutic riding center- I volunteer at one and I think he would be great once he is older.
Yea. There are two ways for a horse to get a club foot, one is genetic and the other is induced (a bone cyst can do it). I don't know what the marker is, but our vet immediately did a complete work over and told us it wasn't in her genes. You can also look back in the horses history. A club foot can skip 2 or 3 generations but if you look back far enough you can see if its a trait. The mare is a registered QH, we have insane amounts of information about her ancestors.
No, there is no genetic marker (at least none known) for a club foot. I would lay money on it being polygenic ;) I think the OP doesn't understand what genetic markers mean (I would say most people wouldn't, so I'm not saying anything bad about you, OP! :) )