Beside King Tut , the rest of the family members did not had any deformations
I suppose the dispute started from the odd way Akhenaten was portraited, even with androgynous features and odd proportions that might had indicated a shape deforming disease. However, that could be dismissed by the way he claimed Aten to be both the father and mother of everything, and that he considered himself as Aten's only son. Studies on this field become increasingly difficult as Akhenaten's written history and artefacts were vandalized/destroyed/altered after his death, leaving space for some level of speculation. Nonetheless, it is most likely Akhenaten didn't have any deformations like his son Tutankhaten had.