Co-Occurring Heterozygous <i>CNOT3</i> and <i>SMAD6</i> Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype

• Main Authors: Priolo Manuela, Radio Francesca Clementina, Pizzi Simone, Pintomalli Letizia, Pantaleoni Francesca, Mancini Cecilia, Cordeddu Viviana, Africa Emilio, Mammì Corrado, Dallapiccola Bruno, Tartaglia Marco
• Format: Article
• Language: English
• Published: MDPI AG 2021-06-01
• Series: Genes
• Subjects: IDDSADF; <i>CNOT3</i>; facial features profiling; <i>SMAD6</i>; aortic coarctation; bicuspid aortic valve
• Online Access: https://www.mdpi.com/2073-4425/12/7/1009

<b>Objective</b>, the application of genomic sequencing in clinical practice has allowed us to appreciate the contribution of co-occurring pathogenic variants to complex and unclassified clinical phenotypes. Besides the clinical relevance, these findings have provided evidence of previously unrecognized functional links between genes in the context of developmental processes and physiology. <b>Patients and Methods</b>, a 5-year-old patient showing an unclassified phenotype characterized by developmental delay, speech delay, peculiar behavioral features, facial dysmorphism and severe cardiopathy was analyzed by trio-based whole exome sequencing (WES) analysis to identify the genomic events underlying the condition. <b>Results</b>, two co-occurring heterozygous truncating variants in <i>CNOT3</i> and <i>SMAD6</i> were identified. Heterozygous loss-of-function variants in <i>CNOT3</i>, encoding a subunit of the CCR4-NOT protein complex, have recently been reported to cause a syndromic condition known as intellectual developmental disorder with speech delay, autism and dysmorphic facies (IDDSADF). Enrichment of rare/private variants in the <i>SMAD6</i> gene, encoding a protein negatively controlling transforming growth factor β/bone morphogenetic protein (TGFB/BMP) signaling, has been described in association with a wide spectrum of congenital heart defects. We dissected the contribution of individual variants to the complex clinical manifestations and profiled a previously unappreciated set of facial features and signs characterizing IDDSADF. <b>Conclusions</b>, two concomitant truncating variants in <i>CNOT3</i> and <i>SMAD6</i> are the cause of the combination of features documented in the patient resulting in the unique multisystem neurodevelopmental condition. These findings provide evidence for a functional link between the CCR4-NOT complex and TGFB/BMP signaling in processes controlling cardiac development. Finally, the present revision provides evidence that IDDSADF is characterized by a distinctive facial gestalt.