Role of hypomorphic variants in variable expressivity of Noonan syndrome

Introduction: Noonan syndrome (NS) is an autosomal dominant multisystem disorder, caused by mutations in RAS pathway’s genes. It’s characterized by a variable expressivity of specific clinical signs including craniofacial anomalies, congenital heart defects, and neurocognitive delay. Interestingly, for 20-30% of patients is not possible to provide molecular diagnosis, suggesting that different genes or mechanisms are involved in NS pathogenesis. Materials and Methods: We studied selected variants from WES analysis of four NS patients negative to the conventional NS mutation screening, through eVai Variant Interpretation platform (enGenome). Patients showed a digenic or compound hetero- zygous inheritance of RAS pathway hypomorphic variants, singularly present in healthy parents (PMID: 32514133). Results: Five heterozygous missense mutations candidate as genetic modifiers passed our filtering steps including variants with MAF less than 0.05 and eVai pathogenicity score at least 3.5, associated with clinical conditions sharing at least 4 Human Phenotype Ontology terms with the patient. A patient showed two variants, one in CACNA1G, a gene related to Spinocerebellar ataxia with autosomal dominant inheritance, and the other one in KDM5B, a gene associated with autosomal recessive mental retardation. In each of the other patients, only one potential pathogenic variant was found. The mutated genes were PC, related to Leigh syndrome inherited as an autosomal recessive trait, SMAD4, with autosomal dominant inheritance in Myhre syndrome, and DDR2, related to Spondylometaphyseal dysplasia caused by recessive mutations. Conclusions: These findings suggest possible modifier genes to be implicated in NS variable expressivity and phenotype severity, providing new insights in the pathogenesis.