Skip to content
Inciteful Med
Resources About us Ask a Question

Building Your Foundation: Understanding Isolated Cleft Palate

Published: | Updated:

At a Glance

An isolated cleft palate (CPO) is an opening in the roof of the mouth that occurs without a cleft lip. It happens when the palate fails to fuse during pregnancy due to genetic and environmental factors. CPO is often missed on prenatal ultrasounds because the palate is hidden by the baby's jaw.

Key Takeaways

  • • Isolated cleft palate is biologically distinct from a cleft lip and develops at a different stage of pregnancy.
  • • A submucous cleft palate is a hidden opening where the surface tissue is intact but the underlying muscles or bone are not properly joined.
  • • Isolated cleft palates are frequently missed on prenatal ultrasounds because the roof of the mouth is obscured by the baby's jaw and tongue.
  • • The condition is multifactorial, caused by a complex combination of genetic inheritance and environmental factors rather than a single event.

If you have just learned that your baby has an isolated cleft palate, you may feel overwhelmed or surprised, especially if your pregnancy scans appeared normal. It is important to know that an isolated cleft palate—often called Cleft Palate Only (CPO)—is a specific condition that is biologically and anatomically different from a cleft lip [1][2]. While this diagnosis brings new challenges, modern medicine has highly effective ways to repair the palate and support your child’s development.

A Distinct Condition

It is a common misconception that a cleft palate is always connected to a cleft lip. In reality, isolated cleft palate (CPO) is considered entirely distinct from cleft lip with or without cleft palate (CL/P) [1].

These two conditions develop at different times during pregnancy. A cleft lip occurs very early in the first trimester when the “primary palate” (the lip and gum line) fails to fuse [3]. In contrast, the “secondary palate” (the roof of the mouth) fuses later in development [4]. Because these structures form at different stages, the genetic and environmental factors that cause them are often different as well [1][5]. Interestingly, CPO is more frequently seen in female infants, whereas cleft lip is more common in males [6].

Understanding the Anatomy

The “palate” is the roof of your mouth, which acts as a barrier between the mouth and the nose. It is divided into two main parts:

  • The Hard Palate: This is the bony front part of the roof of the mouth. A cleft here means there is a physical opening in the bone [7].
  • The Soft Palate: This is the muscular back part of the roof of the mouth. It is responsible for closing off the nose when we speak or swallow [7]. In a soft palate cleft, the muscles (called the velar sling) do not join in the middle. Instead, they attach abnormally to the edge of the bone [8][9].

Submucous Cleft Palate (SMCP)

A submucous cleft palate is a more “hidden” version of a cleft. In these cases, the skin (mucosa) covering the roof of the mouth is intact, but the underlying muscles or bone are not joined correctly [7][10]. Doctors look for a “classic triad” of signs for SMCP: a bifid uvula (the dangling tissue at the back of the throat is split in two), a zona pellucida (a thin, bluish-looking strip in the middle of the palate), and a small, palpable notch in the edge of the hard palate [11][12].

While overt cleft palates are diagnosed immediately at birth (driving immediate feeding protocols), submucous clefts are often undiagnosed until a child is older and develops speech issues (like extreme nasality) or recurrent ear infections [13][14].

Why It Is Often Missed Before Birth

Many parents are confused as to why their routine 20-week ultrasound did not detect the cleft. While a cleft lip is relatively easy for an ultrasound to capture because it is on the baby’s face, the palate is much harder to see [15][16].

The palate is deep inside the mouth and is frequently hidden by the baby’s tongue or jaw [15][17]. Shadows from the facial bones and the baby’s position can also block the view [15]. Because of these technical hurdles, isolated cleft palates are missed prenatally far more often than cleft lips [17].

Why Did This Happen?

If you are wondering if you did something wrong, please know that clefts are multifactorial. This means they are caused by a complex combination of genetics and the environment [18][19].

  • Genetics: Scientists have identified specific genes, such as GRHL3, that play a role in how the palate fuses [5][20]. Often, a baby may have a genetic predisposition that they inherited or that occurred spontaneously [21].
  • Environmental Factors: Certain factors during pregnancy, such as smoking or a lack of folic acid, have been linked to a higher risk of clefts [22][19].

In most cases, it is a “perfect storm” of these factors occurring at the exact moment the palate is trying to close. It is not the result of one single action or choice you made.

Frequently Asked Questions

Is an isolated cleft palate the same as a cleft lip?
No, an isolated cleft palate is a completely distinct condition from a cleft lip. It involves only the roof of the mouth and develops at a different, later stage during pregnancy.
Why didn't my 20-week ultrasound show the cleft palate?
The palate is deep inside the mouth and is often hidden by the baby's tongue, jaw, or facial shadows. Because of these technical hurdles, isolated cleft palates are frequently missed on routine prenatal ultrasounds.
What is a submucous cleft palate?
A submucous cleft is a hidden type of cleft where the skin covering the roof of the mouth is intact, but the muscles or bone underneath did not join correctly. It is often diagnosed later in childhood if a child develops speech issues or recurrent ear infections.
What caused my baby's isolated cleft palate?
Clefts are multifactorial, meaning they result from a complex mix of genetics and environmental factors during early development. It is a biological event that happens when the palate is trying to close, and is not caused by a single action or choice you made.

Questions for Your Doctor

  • • What specific structures are involved in my baby’s cleft—is it the hard palate, the soft palate, or both?
  • • Does my baby have a submucous cleft palate, and if so, how do the 'triad' markers (bifid uvula, zona pellucida, and bony notch) look?
  • • Why was this cleft not visible on our prenatal ultrasounds?
  • • Is this considered a 'nonsyndromic' cleft, and should we meet with a genetic counselor to confirm?
  • • How does the abnormal position of the 'velar sling' muscles in my baby's palate affect their ability to feed or speak later on?
  • • What is the typical timeline for surgical repair for this specific type of isolated cleft palate?

Questions for You

  • • When did you first learn about the cleft palate, and what were your initial thoughts or concerns?
  • • Have you noticed any specific challenges during feeding, such as milk coming through the baby's nose?
  • • Is there any history of clefts, speech issues, or hearing problems in your family tree?
  • • What are your biggest priorities or fears regarding your baby's upcoming treatments or surgeries?

Want personalized information?

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

Feeding Your Baby: Techniques and Specialty Bottles Isolated cleft palate

References

  1. 1

    Non-syndromic cleft palate: Association analysis on three gene polymorphisms of the folate pathway in Asian and Italian populations.

    Carinci F, Palmieri A, Scapoli L, et al.

    International journal of immunopathology and pharmacology 2019; (33()):2058738419858572 doi:10.1177/2058738419858572.

    PMID: 31663447
  2. 2

    Risk prediction models for oral clefts allowing for phenotypic heterogeneity.

    Wen Y, Lu Q

    Frontiers in genetics 2015; (6()):264 doi:10.3389/fgene.2015.00264.

    PMID: 26322076
  3. 3

    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
  4. 4

    Extracellular Matrix Composition and Remodeling: Current Perspectives on Secondary Palate Formation, Cleft Lip/Palate, and Palatal Reconstruction.

    Paiva KBS, Maas CS, Dos Santos PM, et al.

    Frontiers in cell and developmental biology 2019; (7()):340 doi:10.3389/fcell.2019.00340.

    PMID: 31921852
  5. 5

    Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate.

    Mangold E, Böhmer AC, Ishorst N, et al.

    American journal of human genetics 2016; (98(4)):755-62.

    PMID: 27018475
  6. 6

    Prevalence of cleft lip and palate and associated factors in Brazil's Midwest: a single-center study.

    Errari-Piloni C, Barros LAN, Jesuíno FAS, Valladares-Neto J

    Brazilian oral research 2021; (35()):e039 doi:10.1590/1807-3107bor-2021.vol35.0039.

    PMID: 33909861
  7. 7

    Successful treatment of congenital palate perforation: A case report.

    Zhang JF, Zhang WB

    World journal of clinical cases 2020; (8(1)):175-178 doi:10.12998/wjcc.v8.i1.175.

    PMID: 31970184
  8. 8

    Submucous cleft palate: outcomes after primary repair with repositioning of the levator muscle in 51 consecutive patients.

    Smyth AG

    The British journal of oral & maxillofacial surgery 2016; (54(5)):561-7.

    PMID: 26992275
  9. 9

    Intravelar veloplasty in submucous cleft palate without lateral relaxing incision or nasal mucosal incision.

    Sung KP, Lee SH

    International journal of pediatric otorhinolaryngology 2023; (170()):111575 doi:10.1016/j.ijporl.2023.111575.

    PMID: 37178521
  10. 10

    Preliminary Study in Relationship Between Cleft Lip and Palatal Bony Defect in Submucous Cleft Palate.

    Du CJ, Zhou X, Ma L

    The Journal of craniofacial surgery 2022; (33(7)):2024-2027 doi:10.1097/SCS.0000000000008458.

    PMID: 35067530
  11. 11

    Incidence of bifid uvula and its relationship to submucous cleft palate and a family history of oral cleft in the Brazilian population.

    Sales SAG, Santos ML, Machado RA, et al.

    Brazilian journal of otorhinolaryngology 2018; (84(6)):687-690 doi:10.1016/j.bjorl.2017.08.004.

    PMID: 28886940
  12. 12

    High incidence of cleft palate and vomer deformities in patients with Eustachian tube dysfunction.

    Bae SH, Kim JY, Jeong M, et al.

    Scientific reports 2022; (12(1)):10121 doi:10.1038/s41598-022-14011-5.

    PMID: 35710691
  13. 13

    [Velopharyngeal closure pattern and speech performance among submucous cleft palate patients].

    Heng Y, Chunli G, Bing S, et al.

    Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology 2017; (35(3)):296-300 doi:10.7518/hxkq.2017.03.013.

    PMID: 28675016
  14. 14

    CLAPP Classification Scheme and Treatment Algorithm for Submucous Cleft Palate.

    Daiem M, Aslam Khalid F, Turk M, et al.

    The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association 2025; 10556656251341093 doi:10.1177/10556656251341093.

    PMID: 40388926
  15. 15

    Radiology of Cleft Lip and Palate: Imaging for the Prenatal Period and throughout Life.

    Abramson ZR, Peacock ZS, Cohen HL, Choudhri AF

    Radiographics : a review publication of the Radiological Society of North America, Inc 2015; (35(7)):2053-63 doi:10.1148/rg.2015150050.

    PMID: 26562237
  16. 16

    The application of three-dimensional ultrasound with reformatting technique in the diagnosis of fetal cleft lip/palate.

    Ji C, Yang Z, Yin L, et al.

    Journal of clinical ultrasound : JCU 2021; (49(4)):307-314 doi:10.1002/jcu.22994.

    PMID: 33665816
  17. 17

    Cleft palate in fetuses: feasibility of early diagnosis by Crystal and Realistic Vue rendering 3D ultrasound technology in the first trimester.

    Shi Z, Wen H, Leng J, et al.

    Frontiers in pediatrics 2023; (11()):1199965 doi:10.3389/fped.2023.1199965.

    PMID: 37520054
  18. 18

    Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors.

    Martinelli M, Palmieri A, Carinci F, Scapoli L

    Frontiers in cell and developmental biology 2020; (8()):592271 doi:10.3389/fcell.2020.592271.

    PMID: 33195260
  19. 19

    Identification of Novel Variants in Cleft Palate-Associated Genes in Brazilian Patients With Non-syndromic Cleft Palate Only.

    Machado RA, Martelli-Junior H, Reis SRA, et al.

    Frontiers in cell and developmental biology 2021; (9()):638522 doi:10.3389/fcell.2021.638522.

    PMID: 34307341
  20. 20

    Novel susceptibility gene SLC23A2 functions via PI3K-AKT-mTOR pathway in etiology of non-syndromic cleft palate.

    Yin B, Li MJ, Sun JL, et al.

    Journal of human genetics 2025; (70(9)):443-452 doi:10.1038/s10038-025-01352-y.

    PMID: 40456835
  21. 21

    Association between a common missense variant in LOXL3 gene and the risk of non-syndromic cleft palate.

    Khan MFJ, Little J, Mossey PA, et al.

    Congenital anomalies 2018; (58(4)):136-140 doi:10.1111/cga.12288.

    PMID: 29802726
  22. 22

    Maternal-related factors in the origin of isolated cleft palate-A population-based case-control study.

    Ács L, Bányai D, Nemes B, et al.

    Orthodontics & craniofacial research 2020; (23(2)):174-180 doi:10.1111/ocr.12361.

    PMID: 31854100

This page explains isolated cleft palate anatomy and causes for educational purposes. Your pediatrician and specialized cleft care team are the best sources for evaluating and treating your baby's specific condition.

Stay up to date

Get notified when new research about Isolated cleft palate is published.

No spam. Unsubscribe anytime.