According to ComicBook.com on Sept. 6, Marvel's "Agents of "S.H.I.E.L.D." will be using a substitute word in their terminology. Apparently, due to rights issues and reserving terminology for the big screen, the series that is on the horizon will not be using the word "mutant" when referring to whomever they encounter with special abilities. That being said, the term referenced by the show would officially be the "registered gifted" while those not on the list and investigated by Agent Coulson will be obviously coined the term the "unregistered gifted".
It hasn't been confirmed, but said terminology will be made in referenced to the new characters of the cinematic universe such as Scarlet Witch and Quicksilver of the upcoming "Avengers" sequel. This is due in part of rights legalities involving FOX.
There is also a database of characters for the show that the writers will have access to as the series moves forward. Some characters are that of cinematic universe and then others that will be stricken from the show altogether.
"Agents of S.H.I.E.L.D." is set to begin on Sept. 24.