Unraveling the Molecular and Clinical Consequences of an Intragenic TRIP12 Duplication Using Genomic and RNA Analyses

Clark-Baraitser syndrome is a rare neurodevelopmental disorder associated with the E3 ubiquitin-protein ligase gene TRIP12. Using chromosomal microarray analysis (CMA), long-range PCR, breakpoint sequencing, and RNA analyses, we studied a 6-year-old female presenting with developmental delay, aggressive behavior, attention-deficit hyperactivity disorder, and mild dysmorphic features. CMA revealed a de novo ~87 kb copy-number variant (CNV) duplication at 2q36.3, involving Exons 3-14 of TRIP12. Long-range PCR and Sanger sequencing showed a head-to-tail tandem duplication with breakpoints in Introns 2 and 14. RNA analysis identified a novel splicing junction between the coding Exon 14 and the stop codon of the noncoding portion of Exon 3, resulting in a premature translation termination. This suggests the neo-transcript undergoes nonsense-mediated decay and/or produces a truncated protein lacking the critical E6AP-type E3 ubiquitin-protein ligase domain. This case further highlights the challenges with the clinical interpretation of CNV gains and the usefulness of RNA sequencing in the clarification of the impacts of intragenic duplications.