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PubMed This is a summary of 14 peer-reviewed journal articles Updated
Pediatrics

Associated Syndromes and Genetics: CHARGE Syndrome and Beyond

At a Glance

About 50% of choanal atresia cases are linked to genetic conditions, most commonly CHARGE syndrome. Because of this connection, infants require essential screenings like echocardiograms, eye exams, and genetic testing to ensure safe surgical planning and comprehensive care.

When a baby is diagnosed with choanal atresia, one of the first questions doctors ask is whether the blockage is “isolated” or part of a broader “syndrome.” In about 50% of cases, choanal atresia occurs alongside other developmental changes in the body [1]. Understanding these connections is vital because it helps your care team create a comprehensive plan for your baby’s health [2].

CHARGE Syndrome: The Most Common Link

The most frequent syndrome associated with choanal atresia is CHARGE syndrome [1]. This is a complex genetic condition caused by a change (mutation) in the CHD7 gene [3][4]. The name CHARGE is an acronym that stands for its most common features:

  • C: Coloboma (a “gap” or “keyhole” shape in the eye) [5].
  • H: Heart defects (often involving the structures of the heart) [6].
  • A: Atresia choanae (the nasal blockage your baby has) [6].
  • R: Restricted growth and development (delays in physical growth or developmental milestones) [6].
  • G: Genital anomalies (underdeveloped reproductive organs) [6].
  • E: Ear anomalies (uniquely shaped ears or hearing loss) [6].

Because choanal atresia is one of the “major” features of CHARGE, doctors often use the term 3C triad (Coloboma, Choanal atresia, and semicircular Canal anomalies) to refer to the core clinical signs that point toward a CHARGE diagnosis [7].

Beyond CHARGE: Other Genetic Links

While CHARGE is the most common, other genetic conditions can also include choanal atresia:

  • Burn-McKeown Syndrome (BMKS): This is caused by changes in the TXNL4A gene [8]. It often involves choanal atresia along with specific facial features like small ears or a cleft lip [8].
  • Ritscher-Schinzel Syndrome (3C Syndrome): This is a separate condition involving heart defects and specific brain (cerebellum) changes [9][10].
  • Other Syndromes: Conditions like HDR syndrome, Treacher Collins, or Dandy-Walker syndrome may also present with nasal blockages [11][12].

Essential Evaluations for Your Infant

Because choanal atresia can be a “clue” to other internal issues, your baby will need several screenings shortly after birth [1]. These are not “just in case”—they are essential for safe care and surgical planning:

  • Echocardiogram (Heart Ultrasound): To check for heart defects that could affect how your baby handles anesthesia during surgery [1][13].
  • Ophthalmology Exam (Eye Exam): To look for a coloboma, which can sometimes be deep inside the eye and not visible to the naked eye [5].
  • Hearing Test: To evaluate the inner ear and check for semicircular canal anomalies [14][6].
  • Genetic Consultation: A geneticist will look for subtle physical signs and may recommend blood tests to look for the CHD7 or TXNL4A genes [6][8].

Early detection of these associated conditions allows for a highly personalized “roadmap” for your baby’s development and minimizes the risk of complications during their nasal repair [1][2].

Common questions in this guide

Is choanal atresia always part of a genetic syndrome?
No, but in about 50% of cases, it occurs alongside other developmental changes. Because of this high likelihood, doctors will recommend thorough evaluations to check if the nasal blockage is isolated or part of a broader genetic syndrome.
What is CHARGE syndrome?
CHARGE syndrome is a complex genetic condition frequently linked to choanal atresia. It involves multiple features, including eye colobomas, heart defects, growth delays, and ear anomalies, and is usually caused by a mutation in the CHD7 gene.
Why does my baby need an echocardiogram for a nasal blockage?
Because choanal atresia is often linked to genetic syndromes like CHARGE, there is a higher chance of associated heart defects. An echocardiogram ensures your baby's heart is healthy and can safely handle anesthesia during their nasal repair surgery.
What medical tests are needed after a choanal atresia diagnosis?
Your baby will typically need an echocardiogram, an eye exam, a hearing test, and a genetic consultation. These screenings are essential for building a safe, personalized surgical and developmental roadmap for your child.

Questions to Ask Your Doctor

Curated prompts to bring to your next appointment.

  1. 1.Based on my baby's choanal atresia, should we meet with a geneticist to discuss CHD7 or TXNL4A testing?
  2. 2.What specific heart defects are you screening for with the echocardiogram?
  3. 3.Are there any signs of semicircular canal anomalies that might explain why my baby is struggling with balance or hearing?
  4. 4.If my baby is diagnosed with CHARGE syndrome, how will that change our surgical plan for the choanal atresia?
  5. 5.Does the presence of other features, like small ears or eye colobomas, make a syndrome more likely?

Questions For You

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References

References (14)
  1. 1

    [CHARGE syndrome in children with congenital choanal atresia].

    Kotova EN, Bogomilsky MR

    Vestnik otorinolaringologii 2022; (87(3)):7-12 doi:10.17116/otorino2022870317.

    PMID: 35818939
  2. 2

    Diagnostics and therapy of bilateral choanal atresia in association with CHARGE syndrome.

    Koppen T, Bartmann D, Jakob M, et al.

    Journal of neonatal-perinatal medicine 2021; (14(1)):67-74 doi:10.3233/NPM-200450.

    PMID: 32741782
  3. 3

    Identification of a novel heterozygous missense mutation of SEMA3E (c.1327G>A; p. Ala443Thr) in a labor induced fetus with CHARGE syndrome.

    Song X, Wang X, Ding L, et al.

    Molecular genetics & genomic medicine 2020; (8(1)):e1034 doi:10.1002/mgg3.1034.

    PMID: 31691538
  4. 4

    CHARGE syndrome patient with novel CHD7 mutation presenting with severe laryngomalacia and feeding difficulty.

    Lau CL, Chee YY, Chung BHY, Wong MSR

    BMJ case reports 2020; (13(7)) doi:10.1136/bcr-2019-233037.

    PMID: 32699053
  5. 5

    Disseminated Mycobacterium abscessus Infection in a Three-Year-Old Girl With CHARGE Syndrome: A Case Report and Literature Review.

    Hiruma Y, Orimoto R, Sato L, et al.

    Cureus 2025; (17(7)):e88327 doi:10.7759/cureus.88327.

    PMID: 40842793
  6. 6

    Revealing the function of a novel splice-site mutation of CHD7 in CHARGE syndrome.

    Lee B, Duz MB, Sagong B, et al.

    Gene 2016; (576(2 Pt 2)):776-81.

    PMID: 26551301
  7. 7

    Prevalence of Semicircular Canal Hypoplasia in Patients With CHARGE Syndrome: 3C Syndrome.

    Wineland A, Menezes MD, Shimony JS, et al.

    JAMA otolaryngology-- head & neck surgery 2017; (143(2)):168-177 doi:10.1001/jamaoto.2016.3175.

    PMID: 27832265
  8. 8

    Identification of causative variants in TXNL4A in Burn-McKeown syndrome and isolated choanal atresia.

    Goos JAC, Swagemakers SMA, Twigg SRF, et al.

    European journal of human genetics : EJHG 2017; (25(10)):1126-1133 doi:10.1038/ejhg.2017.107.

    PMID: 28905882
  9. 9

    [A phenotypic description of 26 patients with Ritscher-Schinzel syndrome (cranio-cerebello-cardiac dysplasia or 3C syndrome)].

    Pira-Paredes SM, Montoya-Villada JH, Franco-Restrepo JL, et al.

    Revista de neurologia 2017; (64(11)):481-488.

    PMID: 28555453
  10. 10

    Expansion of the CCDC22 associated Ritscher-Schinzel/3C syndrome and review of the literature: Should the minimal diagnostic criteria be revised?

    Gjerulfsen CE, Møller RS, Fenger CD, et al.

    European journal of medical genetics 2021; (64(7)):104246 doi:10.1016/j.ejmg.2021.104246.

    PMID: 34020006
  11. 11

    Familial congenital choanal atresia with GATA3 associated hypoparathyroidism-deafness-renal dysplasia syndrome unidentified on auditory brainstem response.

    Kita M, Kuwata Y, Usui T

    Auris, nasus, larynx 2019; (46(5)):808-812 doi:10.1016/j.anl.2018.10.005.

    PMID: 30396722
  12. 12

    Dandy-Walker syndrome with bilateral choanal atresia: A case report.

    Alsalamah RK, Alenezi MM, Alsaab F

    International journal of surgery case reports 2022; (90()):106702 doi:10.1016/j.ijscr.2021.106702.

    PMID: 34953427
  13. 13

    Anesthesia Management in Patients With Choanal Atresia.

    Yildirim ZB, Akdağ M, Çelik F, Baysal E

    The Journal of craniofacial surgery 2016; (27(8)):1991-1994 doi:10.1097/SCS.0000000000003086.

    PMID: 28005740
  14. 14

    Phenotype and genotype analysis of a French cohort of 119 patients with CHARGE syndrome.

    Legendre M, Abadie V, Attié-Bitach T, et al.

    American journal of medical genetics. Part C, Seminars in medical genetics 2017; (175(4)):417-430 doi:10.1002/ajmg.c.31591.

    PMID: 29178447

This page explains genetic conditions associated with choanal atresia for educational purposes only. Always consult your pediatric geneticist and medical team for appropriate diagnosis, testing, and care planning for your infant.

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