Next-generation sequencing identifies rare variants associated with Noonan syndrome

Abstract

Noonan syndrome (NS) is a relatively common genetic disorder, characterized by typical facies, short stature, developmental delay, and cardiac abnormalities. Known causative genes account for 70-80% of clinically diagnosed NS patients, but the genetic basis for the remaining 20-30% of cases is unknown. We performed nextgeneration sequencing on germ-line DNA from 27 NS patients lacking a mutation in the known NS genes. We identified gainof-function alleles in Ras-like without CAAX 1 (RIT1) and mitogenactivated protein kinase kinase 1 (MAP2K1) and previously unseen loss-of-function variants in RAS p21 protein activator 2 (RASA2) that are likely to cause NS in these patients. Expression of the mutant RASA2, MAP2K1, or RIT1 alleles in heterologous cells increased RAS-ERK pathway activation, supporting a causative role in NS pathogenesis. Two patients had more than one disease-associated variant. Moreover, the diagnosis of an individual initially thought to have NS was revised to neurofibromatosis type 1 based on an NF1 nonsense mutation detected in this patient. Another patient harbored a missense mutation in NF1 that resulted in decreased protein stability and impaired ability to suppress RAS-ERK activation; however, this patient continues to exhibit a NS-like phenotype. In addition, a nonsense mutation in RPS6KA3 was found in one patient initially diagnosed with NS whose diagnosis was later revised to Coffin-Lowry syndrome. Finally, we identified other potential candidates for new NS genes, as well as potential carrier alleles for unrelated syndromes. Taken together, our data suggest that nextgeneration sequencing can provide a useful adjunct to RASopathy diagnosis and emphasize that the standard clinical categories for RASopathies might not be adequate to describe all patients.human genetics | developmental diseases | whole exome sequencing | PTPN11 | RAS

Mutations in RIT1 cause Noonan syndrome with possible juvenile myelomonocytic leukemia but are not involved in acute lymphoblastic leukemia

“…10 In the present study, we identified 30 additional probands and 14 relatives with NS carrying a RIT1 mutation, raising the total number of reported cases to 76. Three variants predicted to be pathogenic in silico were not reported before.…”

“…of 106 patients without mutations in PTPTN11, SOS1, or RAF1, whereas Chen et al 10 have identified five patients with RIT1 mutations after exome sequencing of 25 patients. 10 In the present study, we identified 30 additional probands and 14 relatives with NS carrying a RIT1 mutation, raising the total number of reported cases to 76.…”

“…Aoki et al 8 Bertola et al 15 Chen et al 10 Gos et al Bertola et al 15 Chen et al 10 Gos et al Neonatal auxometry was only computed for babies born at term (37-42 weeks gestation). For growth, SDs were computed by sex.…”

“…18 RIT1 is also involved in the activation of the EPHB2 and MAPK14 pathways upon nerve growth factor signaling, and promotes neuronal development and regeneration. 17 Although RIT1 may not have a major role in normal RAS-ERK pathway activation, the expression of mutant RIT1 alleles in heterologous cells increases MAPK-ERK pathway activation 10 or ELK transactivation, 8 demonstrating a gain-of-function effect and further supporting a causative role for RIT1 in NS pathogenesis.…”

In vivo severity ranking of Ras pathway mutations associated with developmental disorders

“…Although the origins of these phenotypes are still poorly understood, studies of model organisms show that many of the observed structural and functional defects can indeed be mimicked by targeted introduction of mutations found in RASopathies (5). Hundreds of such mutations have already been identified, and many more are likely to be discovered by the sequencing of affected individuals (6).…”