That's never been revealed, either on TV or in any other media.[1] We still don't know which of Susan's parents was the Doctor's child, nor do we know why Susan was travelling with her grandfather but her parents were not.
Some of the earlier novels imply that Susan wasn't actually the Doctor's biological granddaughter, but later novels and audios confirm that she was either his granddaughter, or the granddaughter of the Other, who he's a reincarnation of (and none of that was ever referenced on TV).
- ↑ There was a brief period in the novels when Susan was replaced by Zezanne, whose mother is Miranda, who is either the Doctor's daughter or a more distant descendant. But we know none of that was true for Susan before history changed, or after it changed again.