The diagnosis of PPS has been made in several ethnic groups, including Caucasian, Japanese, and sub-Saharan African. Males and females are equally likely to suffer from the syndrome. Since the disorder is very rare, its incidence rate is difficult to estimate, but is less than 1 in 10,000.

Van der Woude syndrome (VDWS) and popliteal pterygium syndrome (PPS) are allelic variants of the same condition; that is, they are caused by different mutations of the same gene. PPS includes all the features of VDWS, plus popliteal pterygium, syngnathia, distinct toe/nail abnormality, syndactyly, and genito-urinary malformations.

NBCCS has an incidence of 1 in 50,000 to 150,000 with higher incidence in Australia. One aspect of NBCCS is that basal-cell carcinomas will occur on areas of the body which are not generally exposed to sunlight, such as the palms and soles of the feet and lesions may develop at the base of palmar and plantar pits.

One of the prime features of NBCCS is development of multiple BCCs at an early age, often in the teen years. Each person who has this syndrome is affected to a different degree, some having many more characteristics of the condition than others.

Antley–Bixler syndrome, also called trapezoidocephaly-synostosis syndrome, is a rare, very severe autosomal recessive congenital disorder characterized by malformations and deformities affecting the majority of the skeleton and other areas of the body.

The specific cause of camptodactyly remains unknown, but there are a few deficiencies that lead to the condition. A deficient lumbrical muscle controlling the flexion of the fingers, and abnormalities of the flexor and extensor tendons.

A number of congenital syndromes may also cause camptodactyly:

- Jacobsen syndrome

- Beals Syndrome

- Blau syndrome

- Freeman-Sheldon syndrome

- Cerebrohepatorenal syndrome

- Weaver syndrome

- Christian syndrome 1

- Gordon Syndrome

- Jacobs arthropathy-camptodactyly syndrome

- Lenz microphthalmia syndrome

- Marshall-Smith-Weaver syndrome

- Oculo-dento-digital syndrome

- Tel Hashomer camptodactyly syndrome

- Toriello-Carey syndrome

- Stuve-Wiedemann syndrome

- Loeys-Dietz syndrome

- Fryns syndrome

- Marfan's syndrome

- Carnio-carpo-tarsal dysthropy

Möbius syndrome results from the underdevelopment of the VI and VII cranial nerves. The VI cranial nerve controls lateral eye movement, and the VII cranial nerve controls facial expression.

The causes of Möbius syndrome are poorly understood. Möbius syndrome is thought to result from a vascular disruption (temporary loss of bloodflow) in the brain during prenatal development. There could be many reasons that a vascular disruption leading to Möbius syndrome might occur. Most cases do not appear to be genetic. However, genetic links have been found in a few families. Some maternal trauma may result in impaired or interrupted blood flow (ischemia) or lack of oxygen (hypoxia) to a developing fetus. Some cases are associated with reciprocal translocation between chromosomes or maternal illness. In the majority of cases of Möbius syndrome in which autosomal dominant inheritance is suspected, sixth and seventh cranial nerve paralysis (palsy) occurs without associated limb abnormalities.

The use of drugs and a traumatic pregnancy may also be linked to the development of Möbius syndrome. The use of the drugs misoprostol or thalidomide by women during pregnancy has been linked to the development of Möbius syndrome in some cases. Misoprostol is used to induce abortions in Brazil and Argentina as well as in the United States. Misoprostol abortions are successful 90% of the time, meaning that 10% of the time the pregnancy continues. Studies show that the use of misoprostal during pregnancy increases the risk of developing Möbius syndrome by a factor of 30. While this is a dramatic increase in risk, the incidence of Möbius syndrome without misoprostal use is estimated at one in 50000 to 100000 births (making the incidence of Möbius syndrome with misoprostol use, less than one in 1000 births). The use of cocaine (which also has vascular effects) has been implicated in Möbius syndrome.

Some researchers have suggested that the underlying problem of this disorder could be congenital hypoplasia or agenesis of the cranial nerve nuclei. Certain symptoms associated with Möbius syndrome may be caused by incomplete development of facial nerves, other cranial nerves, and other parts of the central nervous system.

There are two distinct genetic mutations associated with the Antley–Bixler syndrome phenotype, which suggests the disorder may be genetically heterogeneous.

Antley–Bixler syndrome is inherited in an autosomal recessive pattern, which means the defective gene is located on an autosome, and two copies of the gene (one inherited from each parent) are required to be born with the disorder. The parents of an individual with an autosomal recessive disorder both carry one copy of the defective gene but are usually not affected by the disorder.

After the last primary tooth is lost, usually around the age of twelve, final orthodontic treatment can be initiated. A patient that has not been able to close or swallow well probably will have an open bite, deficient lower-jaw growth, a narrow archform with crowded teeth, and upper anterior flaring of teeth. Orthognathic (jaw) surgery may be indicated. This should be completed in most situations before the smile surgery where the gracilis muscle is grafted to the face.

Genetic links to 13q12.2 and 1p22 have been suggested.

Focal dermal hypoplasia has been associated with PORCN gene mutations on the X chromosome. 90% of the individuals who are affected with the syndrome are female: the commonly accepted, though unconfirmed, explanation for this is that the non-mosaic hemizygous males are not viable.

The differential diagnosis of focal dermal hypoplasia (Goltz) syndrome includes autosomal recessive Setleis syndrome due to TWIST2 gene mutations. It associated with morning glory anomaly, polymicrogyria, incontinentia pigmenti, oculocerebrocutaneous syndrome, Rothmund-Thomson syndrome and microphthalmia with linear skin defects (also known as MLS) syndrome because they are all caused by deletions or point mutations in the HCCS gene.

Worth syndrome is caused by a mutation in the LRP5 gene, located on human chromosome 11q13.4. The disorder is inherited in an autosomal dominant fashion. This indicates that the defective gene responsible for a disorder is located on an autosome (chromosome 11 is an autosome), and only one copy of the defective gene is sufficient to cause the disorder, when inherited from a parent who has the disorder.

Treatment is usually supportive treatment, that is, treatment to reduce any symptoms rather than to cure the condition.

- Enucleation of the odontogenic cysts can help, but new lesions, infections and jaw deformity are usually a result.

- The severity of the basal-cell carcinoma determines the prognosis for most patients. BCCs rarely cause gross disfigurement, disability or death .

- Genetic counseling

Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

Focal dermal hypoplasia (also known as "Goltz syndrome") is a form of ectodermal dysplasia. It is a multisystem disorder characterized primarily by skin manifestations to the atrophic and hypoplastic areas of skin which are present at birth. These defects manifest as yellow-pink bumps on the skin and pigmentation changes. The disorder is also associated with shortness of stature and some evidence suggests that it can cause epilepsy.

The pattern of inheritance is determined by the phenotypic expression of a gene—which is called "expressivity". Camptodactyly can be passed on through generations in various levels of phenotypic expression, which include both or only one hand. This means that the genetic expressivity is incomplete. It can be inherited from either parent.

In most of its cases, camptodactyly occurs sporadically, but it has been found in several studies that it is inherited as an autosomal dominant condition.

Adducted thumb syndrome recessive form is a rare disease affecting multiple systems causing malformations of the palate, thumbs, and upper limbs. The name Christian syndrome derives from Joe. C. Christian, the first person to describe the condition. Inheritance is believed to be autosomal recessive, caused by mutation in the CHST14 (carbohydrate sulfotransferase 14) gene.

This syndrome is associated with microcephaly, arthrogryposis and cleft palate and various craniofacial, respiratory, neurological and limb abnormalities, including bone and joint defects of the upper limbs, adducted thumbs, camptodactyly and talipes equinovarus or calcaneovalgus. It is characterized by craniosynostosis, and myopathy in association with congenital generalized hypertrichosis.

Patients with the disease are considered intellectually disabled. Most die in childhood. Patients often suffer from respiratory difficulties such as pneumonia, and from seizures due to dysmyelination in the brain's white matter. It has been hypothesized that the Moro reflex (startle reflex in infants) may be a tool in detecting the congenital clapsed thumb early in infancy. The thumb normally extends as a result of this reflex.

Worth syndrome, also known as benign form of Worth hyperostosis corticalis generalisata with torus platinus, autosomal dominant osteosclerosis, autosomal dominant endosteal hyperostosis or Worth disease, is a rare autosomal dominant congenital disorder that is caused by a mutation in the LRP5 gene. It is characterized by increased bone density and benign bony structures on the palate.

There are many potential factors involved.

- Congenital hypopituitarism

- Ectodermal dysplasia

- Down syndrome

- Ionizing radiation to the jaws during tooth development (odontogenesis)

- Chemotherapy during tooth development

- Marshall syndrome

- Rieger syndrome

- Focal dermal hypoplasia

- Silver-Russell syndrome

- Williams syndrome

- Gorlin-Chaudhry-Moss syndrome

- Coffin–Siris syndrome

- Salamon syndrome

- Cleft lip and palate

Others include trichorhinopharyngeal, odontotrichomelic, neuroectodermal and dermo-odontodysplasia syndromes.

Usher syndrome, also known as Hallgren syndrome, Usher-Hallgren syndrome, retinitis pigmentosa-dysacusis syndrome, or dystrophia retinae dysacusis syndrome, is an extremely rare genetic disorder caused by a mutation in any one of at least 11 genes resulting in a combination of hearing loss and visual impairment. It is a leading cause of deafblindness and is at present incurable.

Usher syndrome is classed into three subtypes according to onset and severity of symptoms. All three subtypes are caused by mutations in genes involved in the function of the inner ear and retina. These mutations are inherited in an autosomal recessive pattern.

Since Usher syndrome results from the loss of a gene, gene therapy that adds the proper protein back ("gene replacement") may alleviate it, provided the added protein becomes functional. Recent studies of mouse models have shown one form of the disease—that associated with a mutation in myosin VIIa—can be alleviated by replacing the mutant gene using a lentivirus. However, some of the mutated genes associated with Usher syndrome encode very large proteins—most notably, the "USH2A" and "GPR98" proteins, which have roughly 6000 amino-acid residues. Gene replacement therapy for such large proteins may be difficult.

Females are affected more than males, and the condition occurs in permanent (adult) teeth more than deciduous (baby teeth or milk teeth).

A unibrow is part of normal human variation, but can also stem from developmental disorders. A unibrow is a recognized feature of Cornelia De Lange syndrome, a genetic disorder whose main features include moderate to severe learning difficulties, limb abnormalities such as oligodactyly (fewer than normal fingers or toes) and phocomelia (malformed limbs), and facial abnormalities including a long philtrum (the slight depression/line between the nose and mouth).

Other medical conditions associated with a unibrow include:

- Waardenburg Syndrome;

- Patau Syndrome;

- Smith-Lemli-Opitz Syndrome;

- Sanfilippo Syndrome;

- 3p Deletion Syndrome;

- Chromosome Deletion Dillan 4p Syndrome (Wolf–Hirschhorn Syndrome);

- Gorlin Syndrome (Basal Cell Nevus Syndrome);

- Frontometaphyseal Dysplasia;

- ATRX Syndrome;

- Chromosome 9q34 Microdeletion Syndrome or Kleefstra syndrome.

In the movie City of Angels, Dr. Maggie Rice (played by Meg Ryan) correctly diagnoses the cause of a newborn baby's failure to thrive as due to choanal atresia.

Many environmental conditions have also been known to cause anophthalmia. The strongest support for environmental causes has been studies where children have had gestational-acquired infections. These infections are typically viral. A few known pathogens that can cause anophthalmia are Toxoplasma, rubella, and certain strains of the influenza virus. Other known environmental conditions that have led to anophthalmia are maternal vitamin A deficiency, exposure to X-rays during gestation, solvent abuse, and exposure to thalidomide.

An interstitial deletion of chromosome 14 has been known to occasionally be the source of anophthalmia. The deletion of this region of chromosome has also been associated with patients having a small tongue, and high arched palate, developmental and growth retardation, undescended testes with a micropenis, and hypothyroidism. The region that has been deleted is region q22.1-q22.3. This confirms that region 22 on chromosome 14 influences the development of the eye.