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Copy number variants and their implications for developmental and behavioural problems in cleft lip and/or palate

Alexandros Rammos1,2,3, Rachel Blakey1,2,3, Charlotte A Dennison4,5

  • 1Cleft Collective, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom.

Human Molecular Genetics
|July 15, 2025
PubMed

Insights

Children with cleft lip and/or palate (CL/P) have a higher prevalence of neurodevelopmental copy number variants (CNVs). Identifying these genetic factors aids in the early detection of developmental delays and behavioral issues in affected children.

Area of Science:

  • Genetics
  • Developmental Biology
  • Pediatrics

Background:

  • Cleft lip and/or palate (CL/P) is a common congenital anomaly.
  • CL/P is associated with increased risks of neurodevelopmental and behavioral problems.
  • Shared genetic factors may link CL/P and neurodevelopmental disorders.

Purpose of the Study:

  • To determine the prevalence of neurodevelopmental copy number variants (CNVs) in children with CL/P.
  • To investigate the association between CNVs and early developmental/behavioral problems in CL/P.
  • To compare CNV rates in CL/P to the general population.

Main Methods:

  • Utilized data from the Cleft Collective, a UK national cohort study.
  • Analyzed rates of neurodevelopmental CNVs in children with CL/P.
  • Compared CL/P cohort CNV prevalence with four population-based samples (ALSPAC, BiB, MCS, UK Biobank).
  • Examined differences in CNV prevalence by cleft type (e.g., cleft palate only vs. cleft lip only).
  • Assessed the risk of developmental delays and behavioral problems in CL/P children with and without CNVs.

Main Results:

  • Children with CL/P exhibited a higher prevalence of neurodevelopmental CNVs (3.7%) compared to general population samples (1.7–2.3%).
  • Children with cleft palate only were three times more likely to have a neurodevelopmental CNV than those with cleft lip only.
  • CL/P children with neurodevelopmental CNVs showed increased likelihood of early developmental delays and behavioral problems by age 5.

Conclusions:

  • Neurodevelopmental CNVs are more prevalent in children with CL/P.
  • Specific cleft types, like cleft palate only, have a higher association with CNVs.
  • Genetic testing for CNVs in CL/P may facilitate early identification of developmental needs.

Keywords:
behavioural problemscleft collectivecleft lip and/or palatecopy number variantslongitudinal outcomes

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