A new microdeletion syndrome involving TBC1D24, ATP6V0C, and PDPK1 causes epilepsy, microcephaly, and developmental delay

Genet Med. 2019 May;21(5):1058-1064. doi: 10.1038/s41436-018-0290-3. Epub 2018 Sep 24.


Purpose: Contiguous gene deletions are known to cause several neurodevelopmental syndromes, many of which are caused by recurrent events on chromosome 16. However, chromosomal microarray studies (CMA) still yield copy-number variants (CNVs) of unknown clinical significance. We sought to characterize eight individuals with overlapping 205-kb to 504-kb 16p13.3 microdeletions that are distinct from previously published deletion syndromes.

Methods: Clinical information on the patients and bioinformatic scores for the deleted genes were analyzed.

Results: All individuals in our cohort displayed developmental delay, intellectual disability, and various forms of seizures. Six individuals were microcephalic and two had strabismus. The deletion was absent in all 13 parents who were available for testing. The area of overlap encompasses seven genes including TBC1D24, ATP6V0C, and PDPK1 (also known as PDK1). Bi-allelic TBC1D24 pathogenic variants are known to cause nonsyndromic deafness, epileptic disorders, or DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation, seizures). Sanger sequencing of the nondeleted TBC1D24 allele did not yield any additional pathogenic variants.

Conclusions: We propose that 16p13.3 microdeletions resulting in simultaneous haploinsufficiencies of TBC1D24, ATP6V0C, and PDPK1 cause a novel rare contiguous gene deletion syndrome of microcephaly, developmental delay, intellectual disability, and epilepsy.

Keywords: 16p13.3; Epilepsy; Microcephaly; Microdeletion; TBC1D24.

MeSH terms

  • 3-Phosphoinositide-Dependent Protein Kinases / genetics*
  • Adolescent
  • Adult
  • Child
  • Child, Preschool
  • Chromosome Deletion*
  • Chromosomes, Human, Pair 16
  • Cohort Studies
  • Developmental Disabilities / genetics*
  • Epilepsy / genetics*
  • Female
  • GTPase-Activating Proteins
  • Humans
  • Infant
  • Intellectual Disability / genetics
  • Male
  • Membrane Proteins / genetics*
  • Microcephaly / genetics*
  • Nerve Tissue Proteins / genetics*
  • Syndrome
  • Vacuolar Proton-Translocating ATPases / genetics*
  • Young Adult


  • ATP6V0C protein, human
  • GTPase-Activating Proteins
  • Membrane Proteins
  • Nerve Tissue Proteins
  • TBC1D24 protein, human
  • 3-Phosphoinositide-Dependent Protein Kinases
  • PDPK1 protein, human
  • Vacuolar Proton-Translocating ATPases