Cleft lip

Causes of cleft lip involve both genes and factors in early pregnancy.
Changes in several genes, inherited or new, can raise risk, and family history matters.
Genes set the stage, but environment and lifestyle often decide how the story unfolds.
Known risk factors for cleft lip include smoking, heavy alcohol use, some seizure medicines, and low folate before and during early pregnancy.
Obesity, poorly controlled diabetes, and being male at birth also increase risk.

Genetic risk factors

Cleft lip has a strong genetic component, though the exact cause can vary from family to family. Genetic risk factors for cleft lip range from common DNA differences that nudge risk slightly to rare single-gene or chromosomal changes that can cause a cleft on their own. Some risk factors are inherited through our genes. Even when no specific change is found, family patterns show that shared genes play a major role.

• Family history: Having a parent or sibling with cleft lip increases the chance of a baby being born with a cleft. The likelihood rises when more close relatives are affected.

• Multifactorial pattern: In many families, several genes each contribute a small amount to overall risk. These combined effects can lead to cleft lip even when parents have no features themselves.

• IRF6 changes: Variants in IRF6 are a leading genetic cause and can appear alone or as part of Van der Woude syndrome. They may cause cleft lip by disrupting the signals that guide early lip fusion.

• MSX1 variants: Changes in MSX1 can alter how facial tissues grow and join. Both rare mutations and common variants have been linked to cleft lip with or without cleft palate.

• FOXE1 variants: FOXE1 differences are associated with non-syndromic cleft lip in some families. Effects can range from a small increase in risk to a clearer role when combined with other genes.

• Common risk regions: Variants at 8q24 and in genes such as PAX7 and MAFB are common in the population but slightly raise risk. Several small changes can add up to a meaningful shift in risk for cleft lip.

• Chromosome changes: Large deletions, duplications, or extra chromosomes can disturb facial development pathways. Examples include 22q11.2 deletions and trisomy 13, where cleft lip may occur with other findings.

• Syndromic forms: Cleft lip can be one feature of a genetic syndrome that affects multiple body systems. In these cases, the cleft and other features share a single underlying genetic cause.

• De novo variants: Some babies develop a genetic change for the first time, not present in either parent. These new variants can still cause cleft lip or raise risk.

• Genetic ancestry: Baseline risk varies across populations due to differences in how common certain risk variants are. This reflects genetic background rather than anything parents did or did not do.

• Consanguinity: Parents who are related to each other have a higher chance of carrying the same rare gene change. This can increase the risk of recessive syndromes that include cleft lip.

• Recurrence patterns: Risk tends to be higher when the cleft is more severe or when multiple close relatives are affected. Genetic counseling can help estimate recurrence in future pregnancies.

Transmission

Cleft lip is present at birth and cannot be “caught” from someone else; it is not infectious. It can run in families, most often because several genes together—and conditions early in pregnancy—shift the risk rather than a single gene being passed down on its own. If a parent or sibling has Cleft lip, the chance for another child to be affected is higher than average; in some families a single-gene or chromosome difference explains the pattern, while in others a baby may be the first in the family due to a new genetic change. Because how Cleft lip is inherited can vary by family, a genetics professional can help review your specific chances in future pregnancies.

When to test your genes

Consider genetic testing if there’s a family history of cleft lip or palate, a previous child affected, or you’re planning a pregnancy and want carrier screening. Testing is also reasonable after a prenatal ultrasound suggests a cleft, to check for related syndromes. People with a cleft may test to guide surgical and feeding care.

Families often want to know how life will change after a cleft lip repair, especially in the first few years. For most children with cleft lip, surgery in infancy closes the split and supports normal growth, feeding, and speech development. Some will need additional procedures as they grow—such as minor revisions to improve lip shape or a small touch-up around the nose—but these are usually planned and spaced out over time. Everyone’s journey looks a little different.

Looking at the long-term picture can be helpful. Most people with cleft lip have a typical life span, and the condition itself is not considered life‑limiting. The outlook tends to be excellent when surgery, hearing checks, dental care, and speech support are coordinated early. Many people find that symptoms like feeding difficulties ease quickly after initial repair, though early symptoms of cleft lip can include trouble latching and nasal regurgitation before surgery. If a cleft palate is also present, there’s a higher chance of needing speech therapy or ear tubes; your team will monitor and address these as needed.

With ongoing care, many people maintain strong social, school, and work outcomes. Scars usually fade and blend with natural lip lines over time, and modern surgical techniques aim for balanced facial growth. In medical terms, the long-term outlook is often shaped by both genetics and lifestyle, so your team may discuss family history and, in some cases, offer genetic testing if other features suggest a broader syndrome. Talk with your doctor about what your personal outlook might look like, including how many procedures to expect and the best timing for them.

Cleft lip treatment focuses on repairing the lip, helping with feeding and speech, and supporting facial growth as a child develops. Care is usually coordinated by a cleft team—surgeons, speech-language therapists, dentists/orthodontists, audiologists, and psychologists—with the first lip repair surgery often done in infancy, typically around 3 to 6 months of age. Additional procedures may be needed as a child grows, such as revisions to improve lip shape or nasal symmetry, and orthodontic care to guide teeth and jaw alignment; some children also benefit from speech therapy. Pain relief, scar care, and, when needed, antibiotics are short-term supports around surgery, while orthodontic devices and speech therapy are longer-term tools to optimize function. Not every treatment works the same way for every person, so your doctor can help tailor the plan and timing based on your child’s cleft lip type, overall health, and family goals.

Family history can raise the chance of cleft lip, and for many families the cause is a mix of inherited risk and other factors during early pregnancy. Having a genetic risk is not the same as having the disease itself. Most cases of cleft lip are influenced by several genes, each making a small difference in how the upper lip forms; together, these add up to increase risk. In some families, cleft lip occurs as part of a rare genetic syndrome caused by a single gene change, and the pattern of inheritance may be stronger and may come with other health features. If cleft lip affects more than one relative or appears with other findings, genetic testing and counseling may help look for the genetic causes of cleft lip and clarify chances for future pregnancies. Results rarely give a simple yes-or-no answer, but they can guide planning, including support in a next pregnancy and whether to screen other family members.

Cleft lip can appear alongside other conditions, and these links can shape hearing, feeding, and surgery planning. Doctors call it a “comorbidity” when two conditions occur together. When cleft palate is also present, the risk of fluid buildup in the middle ear and repeated ear infections goes up, which can lead to temporary hearing loss; with an isolated cleft lip, these ear problems are less common. Some babies have cleft lip as part of a broader genetic picture—often called cleft lip associated syndromes—where heart defects, kidney differences, or limb differences may also be found, so teams often recommend heart and kidney checks early on. Dental issues such as missing or extra teeth near the cleft are common and may interact with gum disease or cavities, so coordinated dental care becomes important. Because cleft lip can overlap with other birth differences, shared care between surgeons, pediatricians, audiologists, and dentists helps catch related problems early and guide the safest timing for procedures.

How genes can cause diseases

Humans have more than 20,000 genes, each carrying out one or a few specific functions in the body. One gene instructs the body to digest lactose from milk, another tells the body how to build strong bones and another prevents the body's cells from beginning to multiply uncontrollably and developing into cancer. As all of these genes combined are the building instructions for our body, a defect in one of these genes can have severe health consequences.

Through decades of genetic research, we know the genetic code of any healthy/functional human gene. We have also identified that in certain positions on a gene, some individuals may have a different genetic letter from the one you have. We call these hotspots "Genetic Variations" or "Variants" in short. In many cases, studies have been able to show that having the genetic letter "G" in the position makes you healthy, but having the letter "A" in the same position disrupts the gene function and causes a disease. Genopedia allows you to view these variants in genes and summarizes all that we know from scientific research, which genetic letters (Genotype) have good or bad consequences on your health or on your traits.