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About 20 percent of people with a 9q22.3 microdeletion experience overgrowth (macrosomia), which results in increased height and weight compared to unaffected peers. The macrosomia often begins before birth and continues into childhood. Other physical changes that are sometimes associated with a 9q22.3 microdeletion include the premature fusion of certain bones in the skull (metopic craniosynostosis) and a buildup of fluid in the brain (hydrocephalus). Affected individuals can also have distinctive facial features such as a prominent forehead with vertical skin creases, upward- or downward-slanting eyes, a short nose, and a long space between the nose and upper lip (philtrum).

Many individuals with a 9q22.3 microdeletion have delayed development, particularly affecting the development of motor skills such as sitting, standing, and walking. In some people, the delays are temporary and improve in childhood. More severely affected individuals have permanent developmental disabilities along with intellectual impairment and learning problems. Rarely, seizures have been reported in people with a 9q22.3 microdeletion.

9q22.3 microdeletions also cause the characteristic features of Gorlin syndrome (also known as nevoid basal cell carcinoma syndrome). This genetic condition affects many areas of the body and increases the risk of developing various cancerous and noncancerous tumors. In people with Gorlin syndrome, the type of cancer diagnosed most often is basal cell carcinoma, which is the most common form of skin cancer. Most people with this condition also develop noncancerous (benign) tumors of the jaw, called keratocystic odontogenic tumors, which can cause facial swelling and tooth displacement. Other types of tumors that occur in some people with Gorlin syndrome include a form of childhood brain cancer called a medulloblastoma and a type of benign tumor called a fibroma that occurs in the heart or in a woman's ovaries. Other features of Gorlin syndrome include small depressions (pits) in the skin of the palms of the hands and soles of the feet; an unusually large head size (macrocephaly) with a prominent forehead; and skeletal abnormalities involving the spine, ribs, or skull.

9q22.3 microdeletion is a chromosomal change in which a small piece of chromosome 9 is deleted in each cell. The deletion occurs on the long (q) arm of the chromosome in a region designated q22.3. This chromosomal change is associated with delayed development, intellectual disability, certain physical abnormalities, and the characteristic features of a genetic condition called Gorlin syndrome. [from MedlinePlus Genetics]

In a Number 10 Tessier cleft there is an upper central orbital cleft with a cleft of the middle one-third of the upper eyelid, which often results in total ablepharia. The eyebrow is disrupted, being virtually absent medially, whereas the lateral portion angles upward toward the frontal hairline. There may be ocular anomalies, including colobomata of the iris. The skeletal cleft is through the midportion of the supraorbital rim, the adjacent frontal bone, and the orbital roof lateral to the supraorbital nerve. A frontal encephalocele frequently occupies the frontal bony cleft. The palpebral fissure is grossly elongated with an amblyopic eye displaced inferiorly and laterally. There is also a divergent squint of the right eye. The eyebrow is deficient medially and becomes thinned out laterally , where it is contiguous with a broad downward and forward projection of the frontotemporal hairline (this may be seen in both the Number 9 and 10 clefts.) A broad frontal encephalocele bulges forward from the middle one-third of the right forehead, supraorbital ridge, and orbital roof. The bony cleft, through which the frontal encephalocele presents, involves the anterior half of the orbital roof, the supraorbital rim, and two-thirds of the vertical height of the frontal bone lateral to the supraorbital nerve. The bony orbit is inferiorly displaced and widened with the lateral orbital wall shortened and laterally deviated. Similar distortion of the anterior cranial fossa is evident, being broader and more flattened on the affected side. The calvarium above the level of the cleft and the cranial base below is symmetric. [from HPO]