The cranium consists of three main sections including the base of the cranium (occipital bone), the face (frontal bone), and the top (parietal bones) and sides (temporal bone) of the head. Most of the bones of the cranium are permanently set into place prior to birth. However, the temporal and parietal bones are separated by sutures, which remain open, allowing the head to slightly change in shape during childbirth. The cranial sutures eventually close within the first couple of years following birth, after the brain has finished growing.

In individuals with SCS, the coronal suture separating the frontal bones from the parietal bones, closes prematurely (craniosynostosis), occasionally even before birth. If the coronal suture closes asymmetrically or unilaterally, then the face and forehead will form unevenly, from side-to-side. People with SCS have pointy, tower-like heads because their brain is growing faster than their skull, resulting in increased intracranial pressure (ICP) and causing the top of the head and/or forehead to bulge out to allow for brain growth. The face appears uneven, particularly in the areas of the eyes and cheeks, and the forehead appears wide and tall.

Because of the abnormal forehead, there is less space for the normal facial features to develop. This results in shallow eye sockets and flat cheekbones. The shallow eye sockets make the eyes more prominent or bulging and cause the eyes to be more separated than normal (hypertelorism). The underdeveloped eye sockets, cheekbones, and lower jaw cause the face to appear flat. Furthermore, the minor downward slant of the eyes along with the drooping eyelids (ptosis) adds to the overall unevenness of the face.

Individuals with SCS are all affected differently. Even within the same family, affected individuals have different features. The majority of individuals with SCS are moderately affected, with uneven facial features and a relatively flat face due to underdeveloped eye sockets, cheekbones, and lower jaw. In addition to the physical abnormalities, people with SCS also experience growth delays, which results in a relatively short stature. Although, most individuals with SCS are of normal intelligence, some individuals may have mild to moderate mental retardation (IQ from 50-70). More severe cases of SCS, with more serious facial deformities, occurs when multiple cranial sutures close prematurely.

The syndrome was first reported in an eight-year-old boy, but very few cases have been reported since then. The syndrome is detected by abnormalities noted at birth involving the head, limbs, heart, ears, and skin. It is characterized by premature closure of the fibrous joints between certain bones of the skull in a process known as craniosynostosis. As documented in the first case, the victim tends to suffer from cyanosis and other respiratory and breathing infections, all before the age of one. Body development subsequently slows down, but some problems can be fixed under proper guidance, such as learning to walk with special crutches by five years of age. Craniofacial problems are present that have no effect on the patient's intelligence and mental growth.

Most problems resulting from the syndrome are physical. It causes acrocephaly, making the head appear pointed, and webbing or syndactyly of certain toes or fingers.

Sakati–Nyhan–Tisdale syndrome, also called acrocephalopolysyndactyly type III, is a rare genetic disorder that has been associated with abnormalities in the bones of the legs, congenital heart defects and craniofacial defects. The syndrome belongs to a group of rare genetic disorders known as acrocephalopolysyndactyly or ACPS, for short.