I believe this is sort of like Night Thrasher, of the New Warriors. People (readers) initially suspected he had a mutant-gene also, because White Queen was not able to probe his mind. But it turns out, it was mystical training (of sorts, training is probably the wrong word - perhaps influence?) from Tai (who was also, unbeknownst to all, a powerful mystic in her own right). So while he doesn't have a mutant gene, he has a natural defense from mental probings.
So, since Shaman (Michael) was her father - it probably operates the same way, that her genetic make up does not possess the "X" gene to mark her as an official mutant, but years of being exposed to Shaman and his magic (and possibly subconsciously learning all the moves and words to use magic) has made her a "natural" at using it, thus making it seem it comes from a genetic level (as in generations of powerful shamans/magic users in that family line).