In Season 8, Episode 9 of Futurama, called "Fry Am the Egg Man", Leela says that she has 205 bones in her body. A normal human has 206 (at adulthood), so what bone is Leela missing?
We can see from the image below (from season 6) that Leela's skeleton is completely normal from the neck down. That would strongly imply that the bone that she's missing is within her skull or upper neck.
Presumably she's missing her nasal bone, since that would conflict with her big centrally-located eye.
As Valorum shows, her skeleton from the neck down appears normal. Indeed, the most significant difference between her ("the least-mutated mutant ever born") and a normal person is her one huge eye, suggesting that the one missing bone is part of her facial skeleton.
Since the facial bones are in pairs, the one she is missing is likely an unpaired one, specifically the vomer, which makes sense given the size of her eye and the space it would occupy in her skull.