Craniofacial and Dental Genetics

Teeth begin to develop while a baby is in the mother's womb. By the time a baby is born, they have a full set of formed milk teeth that are lying beneath the gums and ready to emerge over time to help the baby eat.

The growth of the teeth and jawbones is a complex process that is finely regulated by a number of genes. If there are any alterations in the genes that regulate the development of the face, mouth or the teeth, there may be abnormalities in orofacial and dental structures.

Two well known abnormalities that may result from alterations in these genes are orofacial cleft (cleft palate and/or lip) and hypodontia, which refers to a lack of teeth. When more than six teeth are missing, the condition is referred to as oligodontia.

Genetic studies over the past decades have provided tools to help assess the specific genes that could be responsible for these defects. The genes that regulate the development of the structures in the head are very similar across almost all vertebrates, meaning that "knock-out" studies in mice, for example, may be relevant to humans. For such studies, a particular gene is inactivated by replacing it with a piece of artificial DNA. The mice are then monitored for any abnormal development of the head, face and mouth.

Cleft lip and/or palate

The lip is formed during the fourth to seventh week of pregnancy, but if the tissue that forms the lip does not completely join before birth, a cleft will occur and the child is born with an opening in the upper lip. The size of the opening ranges between individuals, with some only appearing as a small slit, while others are large openings. The cleft may be in the middle, one side or both sides of the lip and some children born with this condition may also have a cleft palate. The roof of the mouth develops during the sixth and ninth week of pregnancy but if the tissue that forms the roof does not fully join, the baby is born with a cleft palate. In some babies, there is an opening in both the front and back parts of the palate.

Orofacial clefts that occur in the absence of any major birth defect are one of the most common birth defects in the U.S. The Centers for Disease Control estimates that around 4,440 babies are born with a cleft lip in the U.S each year and 2,650 are born with a cleft palate.
In 2009, researchers from the University of Iowa led an international study that identified a gene that plays an important role in both cleft lip and cleft palate. Previously, the team had established that chromosome 9 is where the gene that causes clefts is located. The 2009 study describes an analysis of DNA from people with a family member affected by cleft lip and/or cleft palate.

The results led to the identification of a single gene on chromosome 9 called FOXE1 that appears to be involved in the development of both cleft lip and cleft palate. Lina Morena, one of the leaders of the study, said the research suggests that the FOXE1 gene is needed for lip formation initially and the for palate formation later on. This finding could lead to improvements in genetic counselling and treatments for the defects.


The congenital absence of teeth is also a very common birth defect and is referred to as hypodontia. When more than six teeth are absent, the term oligodontia is used. Genetic studies conducted using mice have revealed a number of genes that potentially contribute to these conditions, but only three mutations have been identified, namely AXIN2, PAX9 and MSX1. This indicates that hypodontia and oligodontia are complex multifactorial traits influenced by a mixture of gene function, developmental timing and environmental factors.

Mutations in different genes can lead to different forms of oligodontia, where different types of teeth are missing. For example, mutations in MSX1 are always associated with a complete absence of all second premolars and third molars, while mutations in PAX9 are associated with the absence of most permanent molars.

Further Reading

Last Updated: Jan 20, 2023

Sally Robertson

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Sally Robertson

Sally first developed an interest in medical communications when she took on the role of Journal Development Editor for BioMed Central (BMC), after having graduated with a degree in biomedical science from Greenwich University.


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