Environmental factors refer for example to maternal smoking and the maternal exposure to amine-containing drugs. Several research groups have found evidence that these environmental factors are responsible for an increase in the risk of craniosynostosis, likely through effects on fibroblast growth factor receptor genes.

On the other hand, a recent evaluation of valproic acid (an anti-epilepticum), which has been implicated as a causative agent, has shown no association with craniosynostosis.

Certain medication (like amine-containing drugs) can increase the risk of craniosynostosis when taken during pregnancy, these are so-called teratogenic factors.

Biomechanical factors include fetal head constraint during pregnancy. It has been found by Jacob et al. that constraint inside the womb is associated with decreased expression of Indian Hedgehog protein and noggin. These last two are both important factors influencing bone development.

Surgery is needed to prevent the closing of the coronal sutures from damaging brain development. In particular, surgeries for the LeFort III or monobloc midface distraction osteogenesis which detaches the midface or the entire upper face, respectively, from the rest of the skull, are performed in order to reposition them in the correct plane. These surgeries are performed by both plastic and oral and maxillofacial (OMS) surgeons, often in collaboration.

Omphalocele has been described in two patients with Apert syndrome by Herman T.E. et al. (USA, 2010) and by Ercoli G. et al. (Argentina, 2014). An omphalocele is a birth defect in which an intestine or other abdominal organs are outside of the body of an infant because of a hole in the bellybutton area. However, the association between omphalocele and Apert syndrome is not confirmed yet, so additional studies are necessary.

Incidence of Crouzon syndrome is currently estimated to occur in 1.6 out of every 100,000 people. There is a greater frequency in families with a history of the disorder, but that doesn't mean that everyone in the family is affected (as referred to above).

Minor degrees of curvature are common. Reports of incidence vary between 1% and 19.5%.

Clinodactyly is an autosomal dominant trait that has variable expressiveness and incomplete penetrance.

Clinodactyly can be passed through inheritance and presents as either an isolated anomaly or a component manifestation of a genetic syndrome. Many syndromes are associated with clinodactyly, including Down Syndrome, Turner syndrome, Aarskog syndrome, Carpenter syndrome, Seckel syndrome, Cornelia de Lange syndrome, orofaciodigital syndrome 1, 13q deletion syndrome, XXYY syndrome and Silver–Russell syndrome.

When identified prenatally, for example during obstetric ultrasonography, it may be an indication for intrauterine sampling for fetal chromosome analysis as it is statistically correlated with increased risk of chromosome aberration in the fetus.

Dolichocephaly (derived from the Ancient Greek δολιχός, meaning "long") is a condition where the head is longer than would be expected, relative to its width. In humans, scaphocephaly is a form of dolichocephaly.

Dolicocephalic dogs (such as German Shepherds) have elongated noses. This makes them vulnerable to fungal diseases of the nose such as aspergillosis. In humans the anterior–posterior diameter (length) of dolichocephaly head is more than the transverse diameter (width). It has an incidence of 1 in every 4,200 babies.

It can present be in cases of Sensenbrenner syndrome, Crouzon syndrome, Sotos syndrome as well as Marfan syndrome.

Although dolichocephaly may be associated with some other abnormalities, alone it is just a normal variation; unless symptomatic, it is not a cause for concern. Early diagnosis can be made by X-ray or ultrasonography. Treatment is not essential.

Crouzon syndrome is an autosomal dominant genetic disorder known as a branchial arch syndrome. Specifically, this syndrome affects the first branchial (or pharyngeal) arch, which is the precursor of the maxilla and mandible. Since the branchial arches are important developmental features in a growing embryo, disturbances in their development create lasting and widespread effects.

This syndrome is named after Octave Crouzon, a French physician who first described this disorder. He noted the affected patients were a mother and her daughter, implying a genetic basis. First called "craniofacial dysostosis", the disorder was characterized by a number of clinical features. This syndrome is caused by a mutation in the fibroblast growth factor receptor II, located on chromosome 10.

Breaking down the name, "craniofacial" refers to the skull and face, and "dysostosis" refers to malformation of bone.

Now known as Crouzon syndrome, the characteristics can be described by the rudimentary meanings of its former name. What occurs is that an infant's skull and facial bones, while in development, fuse early or are unable to expand. Thus, normal bone growth cannot occur. Fusion of different sutures leads to different patterns of growth of the skull.

Examples include: trigonocephaly (fusion of the metopic suture), brachycephaly (fusion of the coronal suture), dolichocephaly (fusion of the sagittal suture), plagiocephaly (unilateral premature closure of lambdoid and coronal sutures), oxycephaly (fusion of coronal and lambdoidal sutures), Kleeblattschaedel (premature closure of all sutures).

Hypoglossia is a short, incompletely developed tongue. It can occur either as an isolated malformation or in association with other deformities, particularly limb defects in a syndrome known as "oromandibular limb hypogenesis syndrome".

The lateral meningocele syndrome is a very rare skeletal disorder with facial anomalies, hypotonia and meningocele-related neurologic dysfunction.

Empty sella syndrome (abbreviated ESS) is where the pituitary gland shrinks or becomes flattened, filling the sella turcica with cerebrospinal fluid on imaging instead of the normal pituitary. ESS can be found in the diagnostic workup of pituitary disorders, or as an incidental finding when imaging the brain.

This syndrome appears to be inherited in an autosomal dominant fashion.

Molecular analyses suggest that the causative mutations cause a truncation of the protein. These mutations result in the loss of PEST sequence in the protein. This loss is associated with a prolonged half life of the protein.

Mutations in Notch 3 were found to be associated with this syndrome.

If there are symptoms, people with empty sella syndrome can have headaches, as symptoms, which subsides when lying down. Additional symptoms are as follows:

- Abnormality (middle ear ossicles)

- Cryptorchidism

- Dolichocephaly

- Arnold-Chiari type I malformation

- Meningocele

- Patent ductus arteriosus

- Muscular hypotonia

- Platybasia

Hemihypertrophy, now more commonly referred to as hemihyperplasia in the medical literature, is a condition in which one side of the body or a part of one side of the body is larger than the other to an extent considered greater than the normal variation. As it is difficult to establish a set clinical criteria for diagnosis of hemihyperplasia, the dictum is often used that the clinician should be able to see the asymmetry "from the end of the bed".

Hemihyperplasia is a congenital overgrowth disorder and the asymmetry can range from mild to severe. It is important to establish a diagnosis because hemihyperplasia is associated with an increased risk for embryonal tumors, mainly Wilms tumor and hepatoblastoma. Due to the heightened tumor risk, there is a tumor screening protocol that is recommended for all children with isolated hemihyperplasia and Beckwith-Wiedemann Syndrome. Some of the other syndromes associated with hemihyperplasia may also follow this tumor surveillance protocol. The recommended tumor surveillance protocol is:

1. Any child with suspected isolated hemihyperplasia should be referred to a clinical geneticist for evaluation.

2. Abdominal ultrasound every 3 months until 7 years

3. Serum alpha fetoprotein measurement every 3 months until 4 years

4. Daily caretaker abdominal examination at the discretion of the provider/parent

In some cases, children with hemihyperplasia may have different leg lengths. There are two main surgical options for the treatment of uneven leg lengths- shortening and lengthening. Epiphysiodesis, which involves removing part of the growth plate of the longer leg, allowing the shorter leg to "catch up", may be performed on patients still able to grow. Bone resection is performed on patients who have no growth left and involves removing part of the bone. Leg lengthening procedures are more painful, involving the insertion of pins to be turned, moving parts of the bone apart (Ilizarov's Method). This process is reserved mainly for patients with a discrepancy greater than 4 cm, although some leg lengthening procedures are now done cosmetically. Non-surgical options include attachment of a lift to the shoe, allowing the patient to walk normally.

Children with hemihypertrophy may also develop scoliosis, a curvature of the spine.

Hemifacial hyperplasia is believed to be a minor form of hemihypertrophy.

Aniridia is the absence of the iris, usually involving both eyes. It can be congenital or caused by a penetrant injury. Isolated aniridia is a congenital disorder which is not limited to a defect in iris development, but is a panocular condition with macular and optic nerve hypoplasia, cataract, and corneal changes. Vision may be severely compromised and the disorder is frequently associated with a number of ocular complications: nystagmus, amblyopia, buphthalmos, and cataract. Aniridia in some individuals occurs as part of a syndrome, such as WAGR syndrome (kidney nephroblastoma (Wilms tumour), genitourinary anomalies and intellectual disability), or Gillespie syndrome (cerebellar ataxia).

Aniridia may be broadly divided into hereditary and sporadic forms. Hereditary aniridia is usually transmitted in an autosomal dominant manner (each offspring has a 50% chance of being affected), although rare autosomal recessive forms (such as Gillespie syndrome) have also been reported. Sporadic aniridia mutations may affect the WT1 region adjacent to the AN2 aniridia region, causing a kidney cancer called nephroblastoma (Wilms tumor). These patients often also have genitourinary abnormalities and intellectual disability (WAGR syndrome).

Several different mutations may affect the PAX6 gene. Some mutations appear to inhibit gene function more than others, with subsequent variability in the severity of the disease. Thus, some aniridic individuals are only missing a relatively small amount of iris, do not have foveal hypoplasia, and retain relatively normal vision. Presumably, the genetic defect in these individuals causes less "heterozygous insufficiency," meaning they retain enough gene function to yield a milder phenotype.

- AN

- Aniridia and absent patella

- Aniridia, microcornea, and spontaneously reabsorbed cataract

- Aniridia, cerebellar ataxia, and mental deficiency (Gillespie syndrome)

Sensenbrenner syndrome (OMIM #218330) is a rare (less than 20 cases reported by 2010) multisystem disease first described in 1975. It is inherited in an autosomal recessive fashion, and a number of genes appear to be responsible. Three genes responsible have been identified: intraflagellar transport (IFT)122 (WDR10), IFT43 — a subunit of the IFT complex A machinery of primary cilia, and WDR35 (IFT121: TULP4)

It is also known as Sensenbrenner–Dorst–Owens syndrome, Levin Syndrome I and cranioectodermal dysplasia (CED)

Amelogenesis imperfecta hypomaturation type with taurodontism are often confused. Amelogenesis imperfecta of the hypomaturation type with taurodontism (AIHHT) has no hair or bone changes which helps to differentiate between TDO cases and AIHHT. Polymerase chain reaction also known as PCR is used to amply pieces of DNA and observed for the 141 base pair allele as a result of a deletion of four nucleotides in exon 3 of the DLX-3 gene. Additionally, the current research shows that there is heavy reliance on the physical characteristics in the differentiation of TDO verses AIHHT and the severity and prevalence of their expression. For instance, taurodontism is severely expressed in TDO, but mildly expressed in AIHHT. Currently, researchers are trying to identify the reason for the alteration in the DLX-3 and DLX-7 genes that are responsible for AIHHT versus TDO.

Smith–Fineman–Myers syndrome (SFMS1), congenital disorder that causes birth defects. This syndrome was named after 3 men, Richard D. Smith, Robert M. Fineman and Gart G. Myers who discovered it around 1980.

These are pleomorphic and include

- dolichocephaly (with or without sagittal suture synostosis)

- microcephaly

- pre- and postnatal growth retardation

- brachydactyly

- narrow thorax

- rhizomelic dwarfism

- epicanthal folds

- hypodontia and/or microdontia

- sparse, slow-growing, hyperpigmented, fine hair

- nail dysplasia

- hypohydrosis

- chronic renal failure

- heart defects

- liver fibrosis

- visual deficits

- photophobia

- hypoplasia of the posterior corpus callosum

- aberrant calcium homeostasis

Electroretinography shows gross abnormalities.

Two fetuses of 19 and 23 weeks gestation have also been reported. They showed acromesomelic shortening, craniofacial characteristics with absence of craniosynostosis, small kidneys with tubular and glomerular microscopic cysts, persistent ductal plate with portal fibrosis in the liver, small adrenals, an enlarged cisterna magna and a posterior fossa cyst.

SFMS is an X-linked disease by chromosome Xq13. X-linked diseases map to the human X chromosome because this syndrome is an X chromosome linked females who have two chromosomes are not affected but because males only have one X chromosome, they are more likely to be affected and show the full clinical symptoms. This disease only requires one copy of the abnormal X-linked gene to display the syndrome. Since females have two X chromosomes, the effect of one X chromosome is recessive and the second chromosome masks the affected chromosome.

Affected fathers can never pass this X-linked disease to their sons but affected fathers can pass the X-linked gene to their daughters who has a 50% chance to pass this disease-causing gene to each of her children. Since females who inherit this gene do not show symptoms, they are called carriers. Each of the female's carrier's son has a 50% chance to display the symptoms but none of the female carrier's daughters would display any symptoms.

Some patients with SFMS have been founded to have a mutation of the gene in the ATRX on the X chromosome, also known as the Xq13 location. ATRX is a gene disease that is associated with other forms of X-linked mental retardation like Alpha-thalassemia/mental retardation syndrome, Carpenter syndrome, Juberg-Marsidi syndrome, and soastic paraplegia. It is possible that patients with SFMS have Alpha-thalassemia/mental retardation syndrome without the affected hemoglobin H that leads to Alphathalassemia/ mental retardation syndrome in the traditionally recognized disease.

Because the nerve emerges near the bottom of the brain, it is often the first nerve compressed when there is any rise in intracranial pressure. Different presentations of the condition, or associations with other conditions, can help to localize the site of the lesion along the VIth cranial nerve pathway.

The most common causes of VIth nerve palsy in adults are:

- More common: Vasculopathic (diabetes, hypertension, atherosclerosis), trauma, idiopathic.

- Less common: Increased intracranial pressure, giant cell arteritis, cavernous sinus mass (e.g. meningioma, Brain stem Glioblastoma aneurysm, metastasis), multiple sclerosis, sarcoidosis/vasculitis, postmyelography, lumbar puncture, stroke (usually not isolated), Chiari Malformation, hydrocephalus, intracranial hypertension, tuberculosis meningitis.

In children, Harley reports typical causes as traumatic, neoplastic (most commonly brainstem glioma), as well as idiopathic. Sixth nerve palsy causes the eyes to deviate inward (see: Pathophysiology of strabismus). Vallee et al. report that benign and rapidly recovering isolated VIth nerve palsy can occur in childhood, sometimes precipitated by ear, nose and throat infections.

Benign hereditary chorea (BHC), also known as benign familial chorea, is a rare autosomal dominant neurogenetic syndrome. It typically presents in childhood with isolated chorea. Unlike other neurogenetic causes of chorea such as Huntington's disease, BHC is not progressive, and not associated with cognitive decline or psychiatric problems in the vast majority of cases.

BHC is caused by a single-nucleotide insertion mutation in "TITF1", which encodes thyroid transcription factor 1 (TTF-1). This gene is also known as NK2 homeobox 1 (NKX2-1)

In some cases, additional developmental abnormalities of lung and thyroid tissue are found in BHC, leading to the suggested alternative name "brain-lung-thyroid syndrome".

A single copy of the abnormal gene from one parent is able to cause the disease; this is called autosomal dominance. A mutation in the DLX3 gene has been confirmed as the cause of TDO. The onset of TDO begins with a 4 base pair deletion on chromosome 17q21, causing a mutation, specifically frameshift, and the termination codon to be the cause of the lack of complete maturation of the tooth enamel; this mutation is also responsible for the osseous defects in the bone. DLX-3 is expressed in the placenta and is significantly important during embryonic development in regards to hard bone tissue which is present in the teeth, skull, and long bones such as in the arms and legs. During normal tooth development, DLX 3 shifts from predominant expression in the inner enamel epithelium; the outer layer does not express DLX 3. In TDO cases, the DLX-3 is present on the outer enamel epithelium and leads to the dental abnormalities seen in this disease. Improper expression of DLX-3 causes the tooth enamel to be thinner, which leads to attrition and is most often the cause of dental abscess seen in TDO persons.

During osseous, connective tissue, and dermal cell differentiation, DLX 3 in TDO is also responsible for upper cranial thickness, calvaria, osteosclerosis of the long bones, long narrow head (dolichocephaly), abnormally thin brittle nails, and premature closing of fibrous joints. Consequently, 95% of people with TDO that are 16 years old or younger show skeletal abnormalities before full maturation takes place. Lack of mastoid pneumatization by mastoid cells occurs in 82% of the cases and is rarely prevalent outside of TDO diagnosis. Mastoid pneumatization occurs at about 6 months of ages and acts to minimize pressure fluctuations in the Eustachian tubes of the ear. The mastoid lies posterior to the lower jawbone (mandible) and distal to the ear. The Eustachian tube connects the middle ear to the back of the nose, and acts to create a specific pressure in the ear canal that causes vibrations to the eardrum; if adequate pressure is not attained, muffled, dull hearing results. In addition to the mastoid pneumatization assisting the Eustachian tubes for normal hearing, lack of mastoid pneumatization causes inflammation of the ear, general irritation, and does not allow enough air in to assist with mucus flowing out. It is not completely understood why gene mutations occur, but it is known that genetic mutations that cause disease are acquired from either or both parents at fertilization.