Environmental influences may also cause, or interact with genetics to produce, orofacial clefting. An example of how environmental factors might be linked to genetics comes from research on mutations in the gene "PHF8" that cause cleft lip/palate (see above). It was found that PHF8 encodes for a histone lysine demethylase, and is involved in epigenetic regulation. The catalytic activity of PHF8 depends on molecular oxygen, a fact considered important with respect to reports on increased incidence of cleft lip/palate in mice that have been exposed to hypoxia early during pregnancy. In humans, fetal cleft lip and other congenital abnormalities have also been linked to maternal hypoxia, as caused by e.g. maternal smoking, maternal alcohol abuse or some forms of maternal hypertension treatment. Other environmental factors that have been studied include: seasonal causes (such as pesticide exposure); maternal diet and vitamin intake; retinoids — which are members of the vitamin A family; anticonvulsant drugs; nitrate compounds; organic solvents; parental exposure to lead; alcohol; cigarette use; and a number of other psychoactive drugs (e.g. cocaine, crack cocaine, heroin).

Current research continues to investigate the extent to which folic acid can reduce the incidence of clefting.

Genetic counseling for VWS involves discussion of disease transmission in the autosomal dominant manner and possibilities for penetrance and expression in offspring. Autosomal dominance means affected parents have a 50% chance of passing on their mutated "IRF6" allele to a their child. Furthermore, if a cleft patient has lip pits, he or she has a ten times greater risk of having a child with cleft lip with or without cleft palate than a cleft patient who does not have lip pits. Types of clefting between parents and affected children are significantly associated; however, different types of clefts may occur horizontally and vertically within the same pedigree. In cases where clefting is the only symptom, a complete family history must be taken to ensure the patient does not have non-syndromic clefting.

Because the cause of facial clefts still is unclear, it is difficult to say what may prevent children being born with facial clefts. It seems that folic acid contributes to lowering the risk of a child being born with a facial cleft.

Lip pits may be surgically removed either for aesthetic reasons or discomfort due to inflammation caused by bacterial infections or chronic saliva excretion, though spontaneous shrinkage of the lip pits has occurred in some rare cases. Chronic inflammation has also been reported to cause squamous-cell carcinoma. It is essential to completely remove the entire lip pit canal, as mucoid cysts can develop if mucous glands are not removed. A possible side effect of removing the lip pits is a loose lip muscle. Other conditions associated with VWS, including CL, CP, congenital heart defects, etc. are surgically corrected or otherwise treated as they would be if they were non-syndromic.

Many genes associated with syndromic cases of cleft lip/palate (see above) have been identified to contribute to the incidence of isolated cases of cleft lip/palate. This includes in particular sequence variants in the genes "IRF6", "PVRL1" and "MSX1". The understanding of the genetic complexities involved in the morphogenesis of the midface, including molecular and cellular processes, has been greatly aided by research on animal models, including of the genes "BMP4", "SHH", "SHOX2", "FGF10" and "MSX1".

The cause of isolated missing teeth remains unclear, but the condition is believed to be associated with genetic or environmental factors during dental development. Missing teeth have been reported in association with increased maternal age, low birth weight, multiple births and rubella virus infection during embryonic life.

There is a possible correlation between tooth agenesis and innervation. A relationship was also postulated between abnormalities of the brainstem and the presence of agenesis.

Hypodontia is often familial, and can also be associated with genetic disorders such as ectodermal dysplasia or Down syndrome. Hypodontia can also be seen in people with cleft lip and palate.

Among the possible causes are mentioned genetic, hormonal, environmental and infectious.

Cause due to hormonal defects: idiopathic hypoparathyroidism and pseudohypoparathyroidism. Exists the possibility that this defect depends on a moniliasis (candidiasis, "candida endocrinopathy syndrome").

Environmental causes involving exposure to PCBs (ex.dioxin), radiation, anticancer chemotherapeutic agents, allergy and toxic epidermal necrolysis after drug.

Infectious causes of hypodontia: rubella, candida.

The Journal of the American Dental Association published preliminary data suggesting a statistical association between hypodontia of the permanent teeth and epithelial ovarian cancer (EOC). The study shows that women with EOC are 8.1 times more likely to have hypodontia than are women without EOC. The suggestion therefore is that hypodontia can serve as a "marker" for potential risk of EOC in women.

Also the increased frequency of hypodontia in twins and low birth weight in twins with hypodontia suggests that environmental factors during perinatal are responsible hypodontia.

These lesions usually present in neonates, although they may not come to clinical attention until adulthood (for cosmetic reasons). There is no gender predilection. They are present in approximately 3-6 per 1000 live births.

The prevalence has been estimated at 1 in 10,000 births, but exact values are hard to know because some that have the symptoms rarely have Pierre-Robin sequence (without any other associated malformation).

Lip pits are harmless and do not usually require any treatment, although in some reported cases surgical excision has been used.

The nose anomalies found in facial clefts vary. The main goal of the treatment is to reconstruct the nose to get a functional and esthetic acceptable result. A few possible treatment options are to reconstruct the nose with a forehead flap or reconstruct the nasal dorsum with a bone graft, for example a rib graft. The nasal reconstruction with a forehead flap is based on the repositioning of a skin flap from the forehead to the nose. A possible downside of this reconstruction is that once you performed it at a younger age, you can’t lengthen the flap at a later stage. A second operation is often needed if the operation is done on early age, because the nose has a restricted growth in the cleft area. Repair of the ala (wing of the nose) often requires the inset of cartilage graft, commonly taken from the ear.

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

Genetic causes also involve the genes MSX1 and PAX9.

Genetic associations for selective tooth agenesis ("STHAG") include:

OAFNS is a combination of FND and oculo-auriculo-vertebral spectrum (OAVS).

The diagnosis of OAVS is based on the following facial characteristics: microtia (underdeveloped external ear), preauricular tags, facial asymmetry, mandibular hypoplasia and epibulbar lipodermoids (benign tumor of the eye which consists of adipose and fibrous tissue).

There still remains discussion about the classification and the minimal amount of characteristics. When someone presents with FND and the characteristics of OAVS, the diagnosis OAFNS may be made.

As the incidence of OAFNS is unknown, there are probably a lot of children with mild phenotypes that aren’t being diagnosed as being OAFNS.

The cause of OAFNS is unknown, but there are some theories about the genesis. Autosomal recessive inheritance is suggested because of a case with two affected siblings and a case with consanguineous parents. However, another study shows that it is more plausible that OAFNS is sporadic.

It is known that maternal diabetes plays a role in developing malformations of craniofacial structures and in OAVS. Therefore, it is suggested as a cause of OAFNS. Folate deficiency is also suggested as possible mechanism.

Low-dose CT protocols should be considered in diagnosing children with OAFNS.

Craniofrontonasal dysplasia (CFND) is a rare type of FND with X linked inheritance. Multiple features are characteristic for CFND such as craniosynostosis of the coronal sutures (prematurely closed cranial sutures), dry frizzy curled hair, splitting of the nails and facial asymmetry.

There is a large variety in phenotype. Women present with a more severe phenotype than men. Females characteristically have FND, craniosynostosis and additional small malformations. Males are usually more mildly affected, presenting with only hypertelorism. The gene that causes CFND is called EFNB1 and is located on the X chromosome. A hypothesis for the more severe outcome in females is based on X-inactivation, which leads to mosaicism. As a result, patients have less functional cells, generating abnormal tissue boundaries, termed "cellular interference". This process almost never occurs in males, as they have less mutagenic material in their genes. EFBN1 also has an important function in males. As the syndrome has an X-linked inheritance pattern, there is no man-to-man inheritance.

See→ Craniofrontonasal dysplasia for more information

A large number of human gene defects can cause ectrodactyly. The most common mode of inheritance is autosomal dominant with reduced penetrance, while autosomal recessive and X-linked forms occur more rarely. Ectrodactyly can also be caused by a duplication on 10q24. Detailed studies of a number of mouse models for ectrodactyly have also revealed that a failure to maintain median apical ectodermal ridge (AER) signalling can be the main pathogenic mechanism in triggering this abnormality.

A number of factors make the identification of the genetic defects underlying human ectrodactyly a complicated process: the limited number of families linked to each split hand/foot malformation (SHFM) locus, the large number of morphogens involved in limb development, the complex interactions between these morphogens, the involvement of modifier genes, and the presumed involvement of multiple gene or long-range regulatory elements in some cases of ectrodactyly. In the clinical setting these genetic characteristics can become problematic and making predictions of carrier status and severity of the disease impossible to predict.

In 2011, a novel mutation in DLX5 was found to be involved in SHFM.

Ectrodactyly is frequently seen with other congenital anomalies. Syndromes in which ectrodactyly is associated with other abnormalities can occur when two or more genes are affected by a chromosomal rearrangement. Disorders associated with ectrodactyly include Ectrodactyly-Ectodermal Dysplasia-Clefting (EEC) syndrome, which is closely correlated to the ADULT syndrome and Limb-mammary (LMS) syndrome, Ectrodactyly-Cleft Palate (ECP) syndrome, Ectrodactyly-Ectodermal Dysplasia-Macular Dystrophy syndrome, Ectrodactyly-Fibular Aplasia/Hypoplasia (EFA) syndrome, and Ectrodactyly-Polydactyly. More than 50 syndromes and associations involving ectrodactyly are distinguished in the London Dysmorphology Database.

Ectrodactyly can be caused by various changes to 7q. When 7q is altered by a deletion or a translocation ectrodactyly can sometimes be associated with hearing loss. Ectrodactyly, or Split hand/split foot malformation (SHFM) type 1 is the only form of split hand/ malformation associated with sensorineural hearing loss.

The cause of Goldenhar syndrome is largely unknown. However, it is thought to be multifactorial, although there may be a genetic component, which would account for certain familial patterns. It has been suggested that there is a branchial arch development issue late in the first trimester.

An increase in Goldenhar syndrome in the children of Gulf War veterans has been suggested, but the difference was shown to be statistically insignificant.

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.

A congenital lip pit or lip sinus is a congenital disorder characterized by the presence of pits and possibly associated fistulas in the lips. They are often hereditary, and may occur alone or in association with cleft lip and palate, termed Van der Woude syndrome.

It is not known how this abnormality occurs in infants, but one theory is that, at some time during the stage of the formation of the bones of the fetus, the tip of the jaw (mandible) becomes 'stuck' in the point where each of the collar bones (clavicle) meet (the sternum), effectively preventing the jaw bones from growing. It is thought that, at about 12 to 14 weeks gestation, when the fetus begins to move, the movement of the head causes the jaw to "pop out' of the collar bones. From this time on, the jaw of the fetus grows as it would normally, with the result that, when born, the jaw of the baby is much smaller (micrognathia) than it would have been with normal development, although it does continue to grow at a normal rate until the child reaches maturity.

However, association with gene loci 2q24.1-33.3, 4q32-qter, 11q21-23.1, and 17q21-24.3 has been found. Recent studies have indicated that genetic dysregulation of SOX9 gene prevents the SOX9 protein from properly controlling the development of facial structures, which leads to isolated PRS. Similarly, KCNJ2 gene also has a role to play. Overlap with certain other genetic syndromes like Patau syndrome has also been found.

PRS may occur in isolation, but it is often part of an underlying disorder or syndrome. The most common is Stickler Syndrome. Other disorders causing PRS, according to Dr. Robert J. Sphrintzen Ph.D. of the Center for Craniofacial Disorders Montefiore Medical Center, are Velocardiofacial syndrome, Fetal Alcohol Syndrome and Treacher Collins Syndrome. For more disorders associated with PRS see Dr. Sphrintzen's article entitled "The Implications of the Diagnosis of Robin Sequence".

Prevalence ranges from 1 in 3500 to 5600 live births. Male-female ratio is found to be 3:2.

An accessory auricle is considered a developmental anomaly resulting from the persistence of a structure which variably recapitulates the normal external ear.

Twenty to 27% of individuals with a laryngeal cleft also have a tracheoesophageal fistula and approximately 6% of individuals with a fistula also have a cleft. Other congenital anomalies commonly associated with laryngeal cleft are gastro-oesophageal reflux, tracheobronchomalacia, congenital heart defect, dextrocardia and situs inversus. Laryngeal cleft can also be a component of other genetic syndromes, including Pallister-Hall syndrome and G syndrome (Opitz-Friaz syndrome).

In a newborn boy thought to have Fryns syndrome, Clark and Fenner-Gonzales (1989) found mosaicism for a tandem duplication of 1q24-q31.2. They suggested that the gene for this disorder is located in that region. However, de Jong et al. (1989), Krassikoff and Sekhon (1990), and Dean et al. (1991) found possible Fryns syndrome associated with anomalies of chromosome 15, chromosome 6, chromosome 8(human)and chromosome 22, respectively. Thus, these cases may all represent mimics of the mendelian syndrome and have no significance as to the location of the gene for the recessive disorder.

By array CGH, Slavotinek et al. (2005) screened patients with DIH and additional phenotypic anomalies consistent with Fryns syndrome for cryptic chromosomal aberrations. They identified submicroscopic chromosome deletions in 3 probands who had previously been diagnosed with Fryns syndrome and had normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving 15q26.2 (see 142340), and 1 male infant had a deletion in band 8p23.1 (see 222400).

The condition develops in the fetus at approximately 4 weeks gestational age, when some form of vascular problem such as blood clotting leads to insufficient blood supply to the face. This can be caused by physical trauma, though there is some evidence of it being hereditary . This restricts the developmental ability of that area of the face. Currently there are no definitive reasons for the development of the condition.