Phenotypic Correlation Study of RAF1:c.770C>T p.(Ser257Leu) Variant in Noonan Syndrome Patients

Academic Background

Noonan syndrome (NS) is one of the most common RASopathies, primarily caused by the upregulation of RAS protein and mitogen-activated protein kinase (MAPK) signaling pathways. These disorders are characterized by facial dysmorphism, congenital heart defects (CHD) and hypertrophic cardiomyopathy (HCM), growth disturbances, skeletal and ectodermal abnormalities, lymphatic system dysplasia, cryptorchidism, and neurodevelopmental delay/intellectual disability (ID).

In NS patients, hypertrophic cardiomyopathy (HCM) is the main factor contributing to morbidity and mortality. Research shows that gain-of-function mutations in RAF1 are associated with a high incidence of HCM, with the c.770C>T (p.Ser257Leu) variant accounting for about half of the cases and being associated with severe adverse outcomes. However, comprehensive studies on this variant are still lacking. Therefore, this paper aims to define in detail the phenotype of patients with the RAF1:c.770C>T variant and provide a comprehensive phenotypic description through a retrospective analysis of correlative data from 17 unpublished patients and patients reported in the literature.

Research Source

This paper was written by Andrea Gazzin and several other researchers from institutions including the University of Turin, Regina Margherita Children’s Hospital, and Bambino Gesù Children’s Hospital. The study was published in the European Journal of Human Genetics in 2024.

Research Process

Study Subjects and Methods

1. Study Subjects:

   • Patients participating in this study included Noonan syndrome patients carrying the RAF1:c.770C>T mutation who were followed up at various research institutions in Italy from 2010 to 2023.
   • Some of the collected data came from previously published literature.

2. Data Collection:

   • Patient phenotype data was collected through databases such as PubMed, Mastermind, and VarSome, covering the period from 2007 to 2024. Search keywords included “RAF1” and various forms of “770C>T” and “Ser257Leu”.
   • During the data integration process, duplicate literature, preclinical studies, somatic mutations, and other content not meeting the study criteria were excluded, ultimately including 47 papers describing 87 patients.

3. Statistical Analysis:

   • Chi-square tests and Fisher’s exact tests were used to compare differences between groups.
   • Differences between continuous variables were assessed using Student’s t-test, and Kaplan-Meier survival analysis was used to evaluate survival rates.

Experimental Methods

1. Genetic Testing:

   • Next-generation sequencing (NGS) technology was used to analyze patients’ genomic DNA for variants in related genes including BRAF, CBL, HRAS, KRAS, LZTR1, MAP2K1, MAP2K2, etc.

2. Clinical Examinations:

   • Patients underwent repeated cardiac ultrasound examinations to monitor the development of HCM. Diagnosis was determined according to current guidelines.

Data Analysis

• Comparison between the Italian patient cohort and the literature patient cohort revealed differences in birth weight SDS, pregnancy termination rates, central nervous system abnormalities, and ocular defects.
• Further combining the above two groups of data, a total of 107 patients’ data was collected. Analysis showed that 91% of patients had HCM, most diagnosed within the first year of life, and patients had a high early mortality rate (13%).

Research Results

Clinical Features

1. Cardiac Manifestations:

   • 91% of patients developed HCM, with the vast majority diagnosed within the first month after birth.
   • Left ventricular outflow tract obstruction (LVOTO) was present in 55% of patients, with biventricular involvement.

2. Birth and Growth Data:

   • 30% of patients were premature, and 47% of newborns were admitted to the neonatal intensive care unit (NICU).
   • 91% of patients showed short stature, 6% had seizures, and 12% had intellectual disability.

3. Mortality:

   • The main cause of death was complications related to HCM, with an average age of death of 7.5 months.
   • Additionally, a small number of cases (3%) developed malignant tumors.

Research Conclusions

1. Phenotype:

   • Patients with the RAF1:c.770C>T variant exhibit a particularly severe phenotype, primarily characterized by rapidly progressive neonatal HCM and high mortality. The study points out the need for close monitoring and early intervention to prevent or slow the progression of HCM.

2. Clinical Significance:

   • The study provides reliable data for easy reference by clinicians and patient families, aiding in predicting patient prognosis.
   • It emphasizes the superiority of variant-specific studies over gene-specific studies, suggesting more focus on the impact of specific variants on disease phenotypes.

Research Highlights

1. Novelty:

   • This is the first systematic study to evaluate the detailed phenotype and outcomes of patients with the RAF1:c.770C>T variant, providing large-scale data analysis by combining literature and new data.

2. Data Richness:

   • Data from 107 patients was collected and analyzed, making the analysis broadly representative.

3. Clinical Impact:

   • The research results provide scientific basis for early intervention and disease management, helping to improve patient prognosis.

Research Value

• Provides clinicians with comprehensive information on the clinical manifestations and prognosis of the RAF1:c.770C>T variant in Noonan syndrome.
• Emphasizes the importance of variant-specific genetics in disease diagnosis and management, with the potential to promote the development and application of precision medicine.