Skip to content
Inciteful Med

Understanding Cleft Palate: Biology, Causes, and First Steps

Last updated:

A cleft palate occurs when the roof of the mouth doesn't fully fuse during the first 12 weeks of pregnancy. It is highly manageable with specialized care and is usually caused by a combination of genetics and environmental factors, not a single action during pregnancy.

Key Takeaways

  • • A cleft palate forms between the 6th and 12th weeks of pregnancy when the palatal shelves fail to fully fuse together.
  • • Most cleft palates are non-syndromic, meaning the cleft is the only medical finding and the child has no other major health issues.
  • • Submucous cleft palates are hidden beneath the skin of the mouth and are often diagnosed later when speech or feeding issues arise.
  • • Cleft palates are highly manageable, and most children born with the condition go on to lead healthy, typical lives after receiving specialized care.

Receiving a diagnosis of cleft palate can feel overwhelming, but it is important to know that you are not alone. Cleft palate is a common and highly manageable condition [1]. While the global rate for cleft lip and palate is approximately 1 in 700 to 1 in 1,000 births, isolated cleft palate (where the lip is not involved) is slightly rarer, occurring in about 0.2 to 0.7 per 1,000 births depending on the region [2][3].

Most children born with a cleft palate go on to lead healthy, typical lives after receiving care from a specialized medical team. Receiving this diagnosis takes a significant emotional toll, but organizations like the American Cleft Palate-Craniofacial Association (ACPA) offer excellent parent support groups and resources. This guide is designed to help you understand the biology of how a cleft forms and the factors that contribute to it, empowering you for the conversations ahead.

How the Palate Forms

To understand a cleft palate, it helps to look at how a baby develops in the womb. The palate (the roof of the mouth) doesn’t grow as one single piece; instead, it forms from several different parts that must grow toward each other and fuse together [4].

  • The Timeline: The “primary palate” (the front part of the roof of the mouth and the upper lip) finishes forming around the 9th to 10th week of pregnancy [5]. The “secondary palate” (the back part of the roof of the mouth) develops between the 6th and 10th weeks and should be fully fused by the 12th week [6].
  • The Fusion Process: During development, two “palatal shelves” grow out from the sides of the jaw. Initially, they hang vertically on either side of the tongue. As the jaw grows, the tongue moves down, allowing these shelves to flip up into a horizontal position and meet in the middle [4][7].
  • What Happens in a Cleft: A cleft occurs if these shelves are blocked from moving up, if they don’t grow large enough to touch, or if they touch but fail to “stitch” together permanently [8][9].

Types of Cleft Palate

Clefts are categorized based on which structures are involved. This helps doctors determine the best surgical and feeding plans.

  • Cleft Lip and Palate: This involves both the upper lip and the roof of the mouth. It is more common in boys [10].
  • Isolated Cleft Palate (CP): The lip is perfectly formed, but there is an opening in the roof of the mouth. This type is more common in girls and is often harder to detect on a prenatal ultrasound than a cleft lip [10][11].
  • Submucous Cleft Palate (SMCP): This is a “hidden” cleft where the gap is covered by the skin lining (mucosa) of the mouth. It is often diagnosed later, sometimes when a child begins to speak with a “nasal” quality [12]. Doctors look for Calnan’s triad to diagnose this: a bifid uvula (the “dangly bit” at the back of the throat is split), a translucent area in the soft palate, and a small notch in the hard bone of the roof of the mouth [13][14].

Why Does This Happen?

The most important thing to know is that a cleft is rarely caused by any single action or “mistake” during pregnancy. It is usually the result of a complex interaction between genetics and the environment [15].

Genetic Factors

Researchers have identified several genes that play a role in directing the “traffic” of cells during palate formation.

  • IRF6: This is one of the most well-studied genes related to clefting. Variations in this gene can increase the risk of both isolated clefts and those involving the lip [16][17].
  • GRHL3 and PAX9: These genes help control how the skin-like cells of the mouth grow and fuse [18][19].

Environmental Factors

Certain environmental factors can increase the risk, but they usually only cause a cleft if the baby also has a genetic predisposition. These may include certain medications (like some anti-seizure drugs or high doses of retinoic acid) or a lack of specific nutrients like folate during the very early weeks of pregnancy [20][21].

Non-Syndromic vs. Syndromic Clefts

Doctors will work to determine if the cleft is “non-syndromic” or “syndromic.”

  • Non-Syndromic (70-80% of cases): The cleft is the only medical finding. These children generally have no other major health issues [10].
  • Syndromic (20-30% of cases): The cleft is one of several symptoms. For example, in 22q11.2 Deletion Syndrome, a cleft might be paired with heart concerns or immune system differences [22][23]. Another common example is Pierre Robin Sequence, where a specific triad of features is present: a very small lower jaw (micrognathia), a tongue that falls back in the throat (glossoptosis), and an airway obstruction often accompanied by a U-shaped cleft palate. The jaw and tongue position physically block the palate from closing and cause airway obstruction during development [24].

Finding out if a cleft is syndromic helps the medical team provide the most comprehensive care for your child from day one. In many cases, a simple genetic test or a thorough physical exam can provide these answers [23].

Frequently Asked Questions

What is the difference between an isolated cleft palate and a cleft lip and palate?
An isolated cleft palate only involves an opening in the roof of the mouth, while the lip is perfectly formed. A cleft lip and palate involves an opening that affects both the upper lip and the roof of the mouth.
What causes a cleft palate to form?
A cleft palate occurs when the tissues that form the roof of the mouth do not fully fuse together during early pregnancy. This is usually caused by a combination of genetic factors and environmental influences rather than a single event.
What is a submucous cleft palate?
A submucous cleft palate is a 'hidden' opening underneath the skin lining of the roof of the mouth. It is often diagnosed later in childhood when a child begins to speak with a nasal tone or exhibits feeding difficulties.
Does having a cleft palate mean my child has a genetic syndrome?
Not necessarily. In 70 to 80 percent of cases, a cleft palate is non-syndromic, meaning it is the only medical finding and the child has no other major health issues. Your medical team can perform exams and genetic tests to determine if a syndrome is present.
When does the palate form during pregnancy?
The front part of the palate and upper lip finish forming around the 9th to 10th week of pregnancy. The back part of the roof of the mouth develops between the 6th and 10th weeks and should be fully fused by the 12th week.

Questions for Your Doctor

  • • What type of cleft does my child have: is it isolated, part of a cleft lip and palate, or a submucous cleft?
  • • Based on the physical exam, are there any signs (like a small jaw or feeding issues) that might suggest a syndrome or a sequence like Pierre Robin?
  • • Given the diagnosis, do you recommend genetic testing or a consultation with a genetic counselor?
  • • Can you explain the specific 'Calnan’s triad' findings if you suspect a submucous cleft?
  • • Is my child's cleft considered 'non-syndromic,' and how does that change the long-term outlook compared to syndromic cases?

Questions for You

  • • When did we first learn about the diagnosis (prenatally or at birth), and what were our first questions?
  • • Have I noticed any specific signs during feeding, such as milk coming through the nose or difficulty latching?
  • • Does anyone in our extended family have a history of clefts, lip pits, or heart conditions?
  • • What are my biggest concerns right now: is it the surgery, feeding, or how my child will look and speak?

Want personalized information?

Type your question below to get evidence-based answers tailored to your situation.

References

  1. 1

    Current concepts on cleft lip and palate etiology.

    Candotto V, Oberti L, Gabrione F, et al.

    Journal of biological regulators and homeostatic agents 2019; (33(3 Suppl. 1)):145-151. DENTAL SUPPLEMENT.

    PMID: 31538461
  2. 2

    Poverty and Risk of Cleft Lip and Palate: An Analysis of United States Birth Data.

    Vu GH, Warden C, Zimmerman CE, et al.

    Plastic and reconstructive surgery 2022; (149(1)):169-182 doi:10.1097/PRS.0000000000008636.

    PMID: 34936619
  3. 3

    Epidemiology of orofacial clefts in a Danish county over 35 years - Before and after implementation of a prenatal screening programme for congenital anomalies.

    Paaske EB, Garne E

    European journal of medical genetics 2018; (61(9)):489-492 doi:10.1016/j.ejmg.2018.05.016.

    PMID: 29753919
  4. 4

    Gene Regulatory Networks and Signaling Pathways in Palatogenesis and Cleft Palate: A Comprehensive Review.

    Won HJ, Kim JW, Won HS, Shin JO

    Cells 2023; (12(15)) doi:10.3390/cells12151954.

    PMID: 37566033
  5. 5

    PECULIARITIES OF THE HUMAN MAXILLA MORPHOGENESIS.

    Tsyhykalo OV, Kuzniak NB, Dmytrenko RR, et al.

    Wiadomosci lekarskie (Warsaw, Poland : 1960) 2022; (75(10)):2339-2346 doi:10.36740/WLek202210105.

    PMID: 36472258
  6. 6

    Understanding the distinction between cleft lip and cleft palate: a critical step for successful prenatal detection.

    Minor K, Chueh J

    Current opinion in obstetrics & gynecology 2023; (35(2)):113-126 doi:10.1097/GCO.0000000000000852.

    PMID: 36912278
  7. 7

    Observation of the Epithelial Cell Behavior in the Nasal Septum During Primary Palate Closure in Mice.

    Yamamoto S, Kurosaka H, Miura J, et al.

    Frontiers in physiology 2020; (11()):538835 doi:10.3389/fphys.2020.538835.

    PMID: 33123019
  8. 8

    Medial epithelial seam cell migration during palatal fusion.

    Logan SM, Benson MD

    Journal of cellular physiology 2020; (235(2)):1417-1424 doi:10.1002/jcp.29061.

    PMID: 31264714
  9. 9

    Increased miR-200c levels disrupt palatal fusion by affecting apoptosis, cell proliferation, and cell migration.

    Won HJ, Won HS, Shin JO

    Biochemical and biophysical research communications 2023; (664()):43-49 doi:10.1016/j.bbrc.2023.04.090.

    PMID: 37137222
  10. 10

    Variations in Orofacial Clefts.

    Jahanbin A, Jamalinasab A, Niazi AE

    The Journal of craniofacial surgery 2021; (32(2)):e179-e182 doi:10.1097/SCS.0000000000007027.

    PMID: 33705067
  11. 11

    Epidemiology of cleft lip and palate in Bhutan, 2015-2022.

    Tobgyel K, Rai P, Choden K, Gyeltshen T

    BMC oral health 2024; (24(1)):1385 doi:10.1186/s12903-024-05177-7.

    PMID: 39548447
  12. 12

    Analysis of the Chief Complaints at Consultation in 278 Patients With Submucous Cleft Palate.

    Du C, Chen Y, Hua T, et al.

    The Journal of craniofacial surgery 2026; doi:10.1097/SCS.0000000000012476.

    PMID: 41586775
  13. 13

    Management of Congenital Palatal Fistula Associated With Wiskott-Aldrich Syndrome.

    Niimi T, Natsume N, Imura H, et al.

    Cureus 2025; (17(7)):e88137 doi:10.7759/cureus.88137.

    PMID: 40821197
  14. 14

    Impact of anatomical abnormalities on velopharyngeal insufficiency in patients with submucous cleft palate.

    Lee CH, Seo HJ, An JH, et al.

    Journal of plastic, reconstructive & aesthetic surgery : JPRAS 2024; (95()):1-6 doi:10.1016/j.bjps.2024.05.006.

    PMID: 38848650
  15. 15

    IRF6 polymorphisms in Brazilian patients with non-syndromic cleft lip with or without palate.

    Bezerra JF, Silva HPVD, Bortolin RH, et al.

    Brazilian journal of otorhinolaryngology 2020; (86(6)):696-702 doi:10.1016/j.bjorl.2019.04.011.

    PMID: 31495697
  16. 16

    Association of single-nucleotide polymorphisms, rs2235371 and rs2013162, in the IRF6 gene with non-syndromic cleft palate in northeast China.

    Xu W, Han WT, Lu YP, et al.

    Genetics and molecular research : GMR 2016; (15(3)) doi:10.4238/gmr.15038210.

    PMID: 27706679
  17. 17

    Association between variants around IRF6 and non-syndromic orofacial cleft in Western Han Chinese.

    Zhang S, Chen Q, Yang C, et al.

    Oral diseases 2023; (29(3)):1115-1127 doi:10.1111/odi.14100.

    PMID: 34894020
  18. 18

    Lack of Association between Missense Variants in GRHL3 (rs2486668 and rs545809) and Susceptibility to Non-Syndromic Orofacial Clefts in a Han Chinese Population.

    He M, Bian Z

    PloS one 2016; (11(7)):e0159940 doi:10.1371/journal.pone.0159940.

    PMID: 27459192
  19. 19

    The Function and Regulatory Network of Pax9 Gene in Palate Development.

    Li R, Chen Z, Yu Q, et al.

    Journal of dental research 2019; (98(3)):277-287 doi:10.1177/0022034518811861.

    PMID: 30583699
  20. 20

    RNA-seq analysis of palatal transcriptome changes in all-trans retinoic acid-induced cleft palate of mice.

    Peng Y, Wang XH, Su CN, et al.

    Environmental toxicology and pharmacology 2020; (80()):103438 doi:10.1016/j.etap.2020.103438.

    PMID: 32569741
  21. 21

    Evidence of the folate-mediated one-carbon metabolism pathway genes in controlling the non-syndromic oral clefts risks.

    Wang S, Shi J, Liu C, et al.

    Oral diseases 2023; (29(3)):1080-1088 doi:10.1111/odi.14068.

    PMID: 34739175
  22. 22

    Prevalence of 22q11.2 microdeletion syndrome in Iranian patients with cleft palate.

    Nouri N, Memarzadeh M, Salehi M, et al.

    Advanced biomedical research 2016; (5()):201 doi:10.4103/2277-9175.192728.

    PMID: 28217639
  23. 23

    Chromosome 22q11.2 Deletion Syndrome: A Comprehensive Review of Molecular Genetics in the Context of Multidisciplinary Clinical Approach.

    Szczawińska-Popłonyk A, Schwartzmann E, Chmara Z, et al.

    International journal of molecular sciences 2023; (24(9)) doi:10.3390/ijms24098317.

    PMID: 37176024
  24. 24

    Associated syndromes in patients with Pierre Robin Sequence.

    Karempelis P, Hagen M, Morrell N, Roby BB

    International journal of pediatric otorhinolaryngology 2020; (131()):109842 doi:10.1016/j.ijporl.2019.109842.

    PMID: 31927149

This page provides educational information about cleft palate development and causes. It does not replace professional medical advice, diagnosis, or treatment planning from your child's specialized cleft team.

Stay up to date

Get notified when new research about Cleft palate is published.

No spam. Unsubscribe anytime.