My nephew does not have an SSN, when he applied for a job he used an SSN (I do not know if the SSN is invalid).
He does have an ITIN and he would like to know how to file for income taxes using the received W2 with the given SSN but using his ITIN instead.
Thanks for any help.

If he has an SSN he should talk to his employer to have the W2 reissued with the correct SSN. If he doesn't have an SSN he should talk to his employer to have the W2 reissued with his ITIN.