Just the ones that were changed out of spite due to the Fox movie deal (or Dan Slott) Wanda, Pietro, Franklin, Toro and Squirrel Girl. (Although, to be fair I don't really care that much about Toro or Squirrel Girl.)
Characters like Spider-man, Daredevil and the FF already have iconic origins. Turning them into mutants wouldn't make them more interesting, more likely just more convoluted. (We already have a stupid magic spider totem tacked onto the Spider-man origin.)