ClinGen's RASopathy Expert Panel consensus methods for variant interpretation

Purpose

Standardized and accurate variant assessment is essential for effective medical care. To that end, Clinical Genome (ClinGen) Resource clinical domain working groups (CDWG) are systematically reviewing disease-associated genes for sufficient evidence to support disease causality and creating disease-specific specifications of ACMG-AMP guidelines for consistent and accurate variant classification.

Methods

The ClinGen RASopathy CDWG established an expert panel (EP) to curate gene information and generate gene and disease-specific specifications to ACMG-AMP variant classification framework. These specifications were tested by classifying 37 exemplar pathogenic variants plus an additional 66 variants in ClinVar distributed across nine RASopathy genes.

Results

RASopathy-related specifications were applied to sixteen ACMG-AMP criteria, with five also having adjustable strength with availability of additional evidence. Another five criteria were deemed not applicable. Key adjustments to minor allele frequency thresholds, multiple de novo occurrence events and/or segregation, and strength adjustments impacted 60% of variant classifications. Unpublished case-level data from participating laboratories impacted 45% of classifications supporting the need for data sharing.

Conclusions

RAS-specific ACMG-AMP specifications optimized the utility of available clinical evidence and Ras/MAPK pathway-specific characteristics to consistently classify RASopathy-associated variants. These specifications highlight how grouping genes by shared features promotes rapid multi-genic variant assessment without sacrificing specificity and accuracy.

Are RASopathies new monogenic predisposing conditions to the development of systemic lupus erythematosus? Case report and systematic review of the literature

OBJECTIVE

RASopathies (Noonan syndrome (NS) and Noonan-related syndromes) are neurodevelopmental syndromes resulting from germline mutations in genes that participate in the rat sarcoma/mitogen-activated protein kinases (RAS/MAPK) pathway (PTPN11, SOS1, RAF, KRAS or NRAS, and SHOC2). Some monogenic conditions are associated with the development of systemic lupus erythematosus (SLE), and a few reports described the association of SLE with NS. We aim to search for a relationship between RASopathy and the development of SLE.

METHODS

We reported for the first time a case of 13-year-old boy with NS with loose anagen hair (NSLAH) resulting from mutation in SHOC2 who developed an autoimmune disorder that fulfilled four American College of Rheumatology (ACR) criteria for the classification of SLE (polyarthritis, pericarditis, antinuclear antibodies, and anti-DNA antibodies). The case report then prompted a literature review by a systematic search for English and French articles on the subjects of RASopathies and SLE that had English abstracts in PubMed from 1966 to 2012.

RESULTS

We identified seven additional patients with RASopathy and SLE. The male-to-female ratio was 1:1 and age at onset of SLE ranged from 5 to 32 years. The most common features were polyarthritis (7/8 patients), autoimmune cytopenia (4/8 patients), and pericarditis (4/8 patients) while only one patient presented with skin involvement.

CONCLUSION

The association of two rare diseases in eight patients suggests that RASopathies may be associated with the development of SLE, which is characterized by a higher male-to-female ratio, a lower rate of skin involvement, and a higher rate of pericarditis than "classic" SLE.

Hypertrophic Cardiomyopathy in RASopathies: Diagnosis, Clinical Characteristics, Prognostic Implications, and Management

RASopathies are multisystemic disorders caused by germline mutations in genes linked to the RAS/mitogen-activated protein kinase pathway. Diagnosis of RASopathy can be triggered by clinical clues ("red flags") which may direct the clinician toward a specific gene test. Compared with sarcomeric hypertrophic cardiomyopathy, hypertrophic cardiomyopathy in RASopathies (R-HCM) is associated with higher prevalence of congestive heart failure and shows increased prevalence and severity of left ventricular outflow tract obstruction. Biventricular involvement and the association with congenital heart disease, mainly pulmonary stenosis, have been commonly described in R-HCM. The aim of this review is to assess the prevalence and unique features of R-HCM and to define the available therapeutic options.

A PTPN11 allele encoding a catalytically impaired SHP2 protein in a patient with a Noonan syndrome phenotype

The RASopathies are a relatively common group of phenotypically similar and genetically related autosomal dominant genetic syndromes caused by missense mutations affecting genes participating in the RAS/mitogen-activated protein kinase (MAPK) pathway that include Noonan syndrome (NS) and Noonan syndrome with multiple lentigines (NSML, formerly LEOPARD syndrome). NS and NSML can be difficult to differentiate during infancy, but the presence of multiple lentigines, café au lait spots, and specific cardiac defects facilitate the diagnosis. Furthermore, individual PTPN11 missense mutations are highly specific to each syndrome and engender opposite biochemical alterations on the function of SHP-2, the protein product of that gene. Here, we report on a 5-year-old male with two de novo PTPN11 mutations in cis, c.1471C>T (p.Pro491Ser), and c.1492C>T (p.Arg498Trp), which are associated with NS and NSML, respectively. This boy's phenotype is intermediate between NS and NSML with facial dysmorphism, short stature, mild global developmental delay, pulmonic stenosis, and deafness but absence of café au lait spots or lentigines. The double-mutant SHP-2 was found to be catalytically impaired. This raises the question of whether clinical differences between NS and NSML can be ascribed solely to the relative SHP-2 catalytic activity.

NRAS associated RASopathy and embryonal rhabdomyosarcoma

RASopathies are a group of phenotypically overlapping disorders that arise from dysregulation of the RAS/MAPK pathway. These disorders include Noonan syndrome, Costello syndrome, cardiofaciocutaneous syndrome, and neurofibromatosis-Type 1. While somatic mutations in the three human Ras genes (KRAS, HRAS, and NRAS) are a common finding in a variety of cancers, germline mutations in each of the these genes cause developmental RASopathy phenotypes with mutations in specific genes typically correlating with specific phenotypes. We present the case of a germline heterozygous NRAS mutation producing a severe phenotype involving embryonal rhabdomyosarcoma, severe intellectual disability, and numerous melanocytic nevi in addition to more typical manifestations of Noonan syndrome. Additionally, the specific p.G12R NRAS mutation in this case is a common somatic mutation in cancer cells, and analysis of previously reported NRAS-RASopathy cases suggests that mutations at traditionally oncogenic codons are associated with elevated cancer risk not present with mutations at other sites.

RASopathy in Patients With Isolated Sagittal Synostosis

RASopathy is caused by dysfunction in the MAPK pathway, and include syndromes like Noonan syndrome (NS), NS with multiple lentigines (formerly known as Leopard syndrome), cardiofaciocutaneous (CFC), Legius syndrome, capillary malformation–arteriovenous malformation, neurofibromatosis type 1, and Costello syndrome. When counted together, RASopathies affect 1/1000 live births, and are characterized by cardiovascular manifestations, short stature, developmental delay, renal, urogenital, skin/skeletal abnormalities, and dysmorphic appearance. NS—one of the most common RASopathies—occurs in 1/1000 to 1/2500 live births. On the other hand, the frequency of CFC is unknown, but it is one of the rarest RASopathies, with estimates of only a few hundred cases worldwide. However, its phenotype overlaps with that of NS. In this case series, we describe 5 patients with a clinical and genetic diagnosis of RASopathy—either NS or CFC—all of whom were also diagnosed with isolated sagittal synostosis (ISS). Medical records from ophthalmology, cardiology, plastic surgery, medical genetics, cleft craniofacial, and neurosurgery were used to determine patient history. In our cohort, late presentation of ISS was the predominant form of ISS presentation. We hope this report further characterizes the burgeoning relationship between RASopathy and ISS. Furthermore, these findings support including sagittal synostosis among the presenting features in the clinical phenotype of RASopathies. Ethical approval was obtained from the university’s institutional review board.

Molecular Genetics of Noonan Syndrome and RASopathies

The RAS/MAPK signaling pathway plays an essential role in development and tumorigenesis by regulating cell proliferation, differentiation, apoptosis, migration, and metabolism. Therefore, it is not surprising that germline mutations in genes encoding components or regulators of this signaling pathway cause numerous human genetic conditions, including Noonan syndrome and related disorders. The term "RASopathies" has been used to describe these disorders collectively due to their common underlying RAS/MAPK pathway dysregulation and overlapping clinical features. Taken together, the RASopathies represent one of the most common groups of genetic disorders, affecting approximately 1 in 1,000 individuals. This review describes the RAS/MAPK signaling pathway, summarizes multiple molecular genetic approaches used during the last several decades to discover genes responsible for different RASopathies, and finally focuses on several major disease genes associated with Noonan syndrome and related disorders with regard to genomic locations, structure, mutations, and genotype-phenotype correlations.

Objective differential diagnosis of Noonan and Williams-Beuren syndromes in diverse populations using quantitative facial phenotyping

Introduction

Patients with Noonan and Williams–Beuren syndrome present similar facial phenotypes modulated by their ethnic background. Although distinctive facial features have been reported, studies show a variable incidence of those characteristics in populations with diverse ancestry. Hence, a differential diagnosis based on reported facial features can be challenging. Although accurate diagnoses are possible with genetic testing, they are not available in developing and remote regions.

Methods

We used a facial analysis technology to identify the most discriminative facial metrics between 286 patients with Noonan and 161 with Williams‐Beuren syndrome with diverse ethnic background. We quantified the most discriminative metrics, and their ranges both globally and in different ethnic groups. We also created population‐based appearance images that are useful not only as clinical references but also for training purposes. Finally, we trained both global and ethnic‐specific machine learning models with previous metrics to distinguish between patients with Noonan and Williams–Beuren syndromes.

Results

We obtained a classification accuracy of 85.68% in the global population evaluated using cross‐validation, which improved to 90.38% when we adapted the facial metrics to the ethnicity of the patients (p = 0.024).

Conclusion

Our facial analysis provided for the first time quantitative reference facial metrics for the differential diagnosis Noonan and Williams–Beuren syndromes in diverse populations.

Recurrent ganglioneuroma in PTPN11-associated Noonan syndrome: A case report and literature review

Noonan syndrome (NS) is an autosomal dominant condition with variable expressivity most commonly due to a germline pathogenic variant in PTPN11, which encodes the protein tyrosine phosphatase SHP-2. Gain-of-function variants in PTPN11 are known to promote oncogenic behavior in affected tissues. We report the clinical description of a young adult male presenting with relapsing ganglioneuromas, dysmorphic features, cardiac abnormalities, and multiple lentigines, strongly suspicious for NS. Solid tumor testing identified the recurrent pathogenic c.922G>A (p.Asn308Asp) in PTPN11. Proband and parental blood sampling testing confirmed c.922G>A as a de novo germline alteration. Comprehensive literature review of solid tumors specifically associated to PTPN11, indicates that this is the first documentation of ganglioneuroma and its clinical recurrence after resection in conjunction with a genetically confirmed NS diagnosis. The findings in our patient further extend the list of neuroblastic and neural crest-derived neoplasms associated with this condition.

Craniofacial and cutaneous findings in Noonan, Costello and LEOPARD syndromes

Noonan, Costello and LEOPARD syndromes belong to a family of cardiofaciocutaneous disorders and share common genetic traits. As they are associated with a germline mutation in genes encoding proteins involved in RAS/MAPK, patients suffering from these syndromes are at a greater risk of cancer and abnormal myelopoiesis in infancy. Patients with cardio faciocutaneous syndromes share some clinically overlapping syndromes, therefore differential diagnosis can be problematic. In this paper we aim at demonstrating distinctive craniofacial and cutaneous manifestations of Noonan, Costello and LEOPARD syndromes which can be useful for clinicians who aim at treatment of children with rare diseases.

Extending the prenatal Noonan's phenotype by review of ultrasound and autopsy data

OBJECTIVES

The antenatal phenotypic spectrum of Noonan Syndrome (NS) requires better characterization.

METHODS

This multicenter retrospective observational included 16 fetuses with molecularly confirmed NS admitted for fetopathological examination between 2009 and 2016.

RESULTS

Among 12 pathogenic variants (PV) in PTPN11 (80%), 5 (42%) fell between position c.179 and c.182. Ultrasound showed increased nuchal translucency (n=13/16, 93%), increased nuchal fold after 15 weeks of gestation (n=12/16, 75%), pleural effusions (n=11/16, 69%), polyhydramnios (n=9/16, 56%), hydrops (n=7/16, 44%), cardiovascular (n=6/16, 38%) and cerebral (n=4/16, 25%) anomalies. Fetopathological examination found dysmorphic features in all cases, cardiovascular anomalies (n=12/15, 80%), pulmonary hypoplasia (n=10/15, 67%), effusions (n=7/15, 47%) and neuropathological anomalies (n=5/15, 33%). Hydrops was significantly (p=0.02) more frequent in the four fetuses with RIT1, NRAS and RAF1 PV versus the 12 fetuses with PTPN11 PV.

CONCLUSIONS

Increased nuchal translucency and nuchal fold is common in NS. NS antenatal phenotype showed high in utero fetal death, hydrops, prenatal pleural effusion and pulmonary hypoplasia, although the inclusion of only deceased fetuses will have selected more severe phenotypes. Non-specific cardiovascular and neurological abnormalities should be added to NS antenatal phenotype. Next generation sequencing will help detect more genotypes, clarifying the prenatal phenotype and identifying genotype-phenotype correlations. This article is protected by copyright. All rights reserved.

Diagnostic challenge of cutis Verticis Gyrata (CVG) in a patient presenting clinical features of Noonan or turner syndrome

Cutis Verticis Gyrata (CVG) is an uncommon condition, often classified as primary (idiopathic) or secondary to other diseases or syndromes. Its pathogenesis remains poorly understood, and its association with genetic syndromes is particularly rare. Noonan and Turner syndromes are distinct genetic disorders with characteristic phenotypes and multiple systemic involvements. This report aims to highlight the diagnostic complexities when CVG presents in the backdrop of these syndromes. A 38 years old patient was presented with chief complaints of receding hairline, dropping eyelids, cerebral deformations with deep furrows and thickened dermis. On the basis of patient's complaints, Noonan or turner syndrome was considered as possible diagnosis. This particular report presents a case of patient suffering from CVG having history of noonan and turner syndrome. With the detailed MRI, histology etc. CVG was finally confirmed. The novelty of this case lies in its rarity, diagnostic complexity, and the need for a multidisciplinary approach to unravel and manage the intersecting conditions. It contributes valuable insights to the existing medical literature, enhancing our understanding of the interplay between dermatological and genetic conditions. Patients with Noonan and turner syndrome exhibit clinical signs and symptoms that are strikingly similar to those of CVG, suggesting that this presents a significant diagnostic problem. An unfavorable outcome could arise from delayed or incorrect diagnosis. Because of this, it is recommended that healthcare fraternities should include uncommon illnesses like CVG as differential diagnosis. Considering CVG in differential diagnosis is crucial for early identification, accurate diagnosis, and comprehensive management. It ensures that associated systemic and genetic conditions are not overlooked and that patients receive holistic and personalized care.

Helsmoortel-Van der Aa Syndrome-Cardiothoracic and Ectodermal Manifestations in Two Patients as Further Support of a Previous Observation on Phenotypic Overlap with RASopathies

The ADNP-gene-related neurodevelopmental disorder Helsmoortel-Van der Aa syndrome is a rare syndromic-intellectual disability-an autism spectrum disorder first described by Helsmoortel and Van der Aa in 2014. Recently, a large cohort including 78 patients and their detailed phenotypes were presented by Van Dijck et al., 2019, who reported developmental delay, speech delay and autism spectrum disorder as nearly constant findings with or without variable cardiological, gastroenterological, urogenital, endocrine and neurological manifestations. Among cardiac malformations, atrial septal defect, patent ductus arteriosus, patent foramen ovale and mitral valve prolapse were the most common findings, but other unspecified defects, such as mild pulmonary valve stenosis, were also described. We present two patients with pathogenic ADNP variants and unusual cardiothoracic manifestations-Bland-White-Garland syndrome, pectus carinatum superiorly along the costochondral junctions and pectus excavatum inferiorly in one patient, and Kawasaki syndrome with pericardiac effusion, coronary artery dilatation and aneurysm in the other-who were successfully treated with intravenous immunoglobulin, corticosteroid and aspirin. Both patients had ectodermal and/or skeletal features overlapping those seen in RASopathies, supporting the observations of Alkhunaizi et al. 2018. on the clinical overlap between Helsmoortel-Van der Aa syndrome and Noonan syndrome. We observed a morphological overlap with the Noonan-like disorder with anagen hair in our patients.

Treatment of Facial Lentigines in an Adult Female Patient Suspected with Leopard Overlap Noonan Syndrome

Lentigines are defined as multiple small pigmented macules measuring up to one centimeter and surrounded by normal-appearing skin, commonly caused by genetic factors. LEOPARD syndrome (LS) is an autosomal dominant distinguished by the presence of several lentigines, with specific phenotypic characteristics that resembles Noonan syndrome (NS). LS is likely to be underdiagnosed or misdiagnosed because many of its symptoms are minor and the accurate diagnosis may be overlooked. Therapy for lentigines are generally aimed at tackling aesthetic disfigurement and its subsequent psychological impacts. This case report aims to highlight the efficacy of 532-nanometer (nm) Q-switched (QS) Nd:YAG laser in treating lentigines in a 21-year-old woman with LS overlap NS. The patient initially came to seek treatment of her facial lentigines. However, some mild abnormalities such as ocular hypertelorism, left eye ptosis, and webbed neck were observed. Hormonal, cardiac, and pulmonary functions were within normal limit. Histopathological results supported the diagnosis of lentigo. The patient was given sunscreen and depigmenting agents and was instructed to apply the medications routinely. The patient then underwent two sessions of 532-nm QS Nd:YAG laser with a 3 mm spot size, 1 J/cm² fluence, and a 1 Hz frequency. Objective clinical improvements were observed using spectrophotometer examination, there were no side effects found, and she was satisfied with the results. Dermatologists should play an integral role in establishing the diagnosis and management of systemic syndrome, manifesting specifically as dermatological symptoms. Lentigines in LS last throughout the patient's lifespan. Nd:YAG laser therapy can be effective in treating lentigines with long-lasting results. It plays a role in improving the patient's life quality, especially where the genetic disorder itself is a debilitating condition. The limitation of this case report was the lack of a genetic test, as the suspected diagnosis was made based on clinical symptoms.

Natural history and outcomes in paediatric RASopathy-associated hypertrophic cardiomyopathy

AIMS

This study aimed to describe the natural history and predictors of all-cause mortality and sudden cardiac death (SCD)/equivalent events in children with a RASopathy syndrome and hypertrophic cardiomyopathy (HCM).

METHODS AND RESULTS

This is a retrospective cohort study from 14 paediatric cardiology centres in the United Kingdom and Ireland. We included children <18 years with HCM and a clinical and/or genetic diagnosis of a RASopathy syndrome [Noonan syndrome (NS), NS with multiple lentigines (NSML), Costello syndrome (CS), cardiofaciocutaneous syndrome (CFCS), and NS with loose anagen hair (NS-LAH)]. One hundred forty-nine patients were recruited [111 (74.5%) NS, 12 (8.05%) NSML, 6 (4.03%) CS, 6 (4.03%) CFCS, 11 (7.4%) Noonan-like syndrome, and 3 (2%) NS-LAH]. NSML patients had higher left ventricular outflow tract (LVOT) gradient values [60 (36-80) mmHg, P = 0.004]. Over a median follow-up of 197.5 [inter-quartile range (IQR) 93.58-370] months, 23 patients (15.43%) died at a median age of 24.1 (IQR 5.6-175.9) months. Survival was 96.45% [95% confidence interval (CI) 91.69-98.51], 90.42% (95% CI 84.04-94.33), and 84.12% (95% CI 75.42-89.94) at 1, 5, and 10 years, respectively, but this varied by RASopathy syndrome. RASopathy syndrome, symptoms at baseline, congestive cardiac failure (CCF), non-sustained ventricular tachycardia (NSVT), and maximal left ventricular wall thickness were identified as predictors of all-cause mortality on univariate analysis, and CCF, NSVT, and LVOT gradient were predictors for SCD or equivalent event.

CONCLUSIONS

These findings highlight a distinct category of patients with Noonan-like syndrome with a milder HCM phenotype but significantly worse survival and identify potential predictors of adverse outcome in patients with RASopathy-related HCM.

Clinical Manifestations of Noonan Syndrome and Related Disorders

Noonan syndrome represents a heterogeneous group of genetic disorders caused by mutations in genes of the RAS/MAPK pathway. Related syndromes include cardiofaciocutaneous syndrome, Noonan syndrome with multiple lentigines and Costello syndrome. The common phenotypic features of Noonan syndrome include facial dysmorphisms, short stature, congenital heart defects and genitourinary abnormalities. These and other findings as well as features of related disorders are discussed. In addition we briefly review clinical diagnosis and prenatal findings of these syndromes and genetic counseling implications.

Cardiac screening in pediatric patients with neurofibromatosis type 1: similarities with Noonan syndrome?

Both Neurofibromatosis type 1 (NF1) and Noonan syndrome (NS) are RASopathies. Characteristic cardiac phenotypes of NS, including specific electrocardiographic changes, pulmonary valve stenosis and hypertrophic cardiomyopathy have not been completely studied in NF1.

PURPOSE

The aims of this study were to assess: (1) similarities in the prevalence and types of ECG and conventional echocardiographic findings described in NS in asymptomatic patients with NF1, and (2) the presence of discrete myocardial dysfunction in NF1 patients using myocardial strain imaging.

METHODS

Fifty-eight patients with NF1 (ages 0-18 years), and thirty-one age-matched healthy controls underwent cardiac assessment including blood pressure measurements, a 12-lead ECG, and detailed echocardiography. Quantification of cardiac chamber size, mass and function were measured using conventional echocardiography. Myocardial strain parameters were assessed using 2-Dimensional (2D) Speckle tracking echocardiography.

RESULTS

Asymptomatic patients with NF1 had normal electrocardiograms, none with the typical ECG patterns described in NS. However, patients with NF1 showed significantly decreased calculated Z scores of the left ventricular internal diameter in diastole and systole, reduced left ventricular mass index and a higher incidence of cardiac abnormal findings, mainly of the mitral valve, in contrast to the frequently described types of cardiac abnormalities in NS. Peak and end systolic global circumferential strain were the only significantly reduced speckle tracking derived myocardial strain parameter.

CONCLUSIONS

Children with NF1 demonstrated more dissimilarities than similarities in the prevalence and types of ECG and conventional echocardiographic findings described in NS. The role of the abnormal myocardial strain parameter needs to be explored.

Skeletal defects and bone metabolism in Noonan, Costello and cardio-facio-cutaneous syndromes

Noonan, Costello and Cardio-facio-cutaneous syndromes belong to a group of disorders named RASopathies due to their common pathogenetic origin that lies on the Ras/MAPK signaling pathway. Genetics has eased, at least in part, the distinction of these entities as they are presented with overlapping clinical features which, sometimes, become more pronounced with age. Distinctive face, cardiac and skeletal defects are among the primary abnormalities seen in these patients. Skeletal dysmorphisms range from mild to severe and may include anterior chest wall anomalies, scoliosis, kyphosis, short stature, hand anomalies, muscle weakness, osteopenia or/and osteoporosis. Patients usually have increased serum concentrations of bone resorption markers, while markers of bone formation are within normal range. The causative molecular defects encompass the members of the Ras/MAPK/ERK pathway and the adjacent cascades, important for the maintenance of normal bone homeostasis. It has been suggested that modulation of the expression of specific molecules involved in the processes of bone remodeling may affect the osteogenic fate decision, potentially, bringing out new pharmaceutical targets. Currently, the laboratory imprint of bone metabolism on the clinical picture of the affected individuals is not clear, maybe due to the rarity of these syndromes, the small number of the recruited patients and the methods used for the description of their clinical and biochemical profiles.

Atypical left-ventricular hypertrophy with apical aneurysm in leopard syndrome

Noonan Syndrome with Multiple Lentigines (NSML-formerly known as LEOPARD syndrome) is a rare autosomal dominant condition that usually exhibits cardiac involvement with hypertrophic cardiomyopathy (HCM). Here we present a case of a NSML patient with an unusual and patchy cardiac hypertrophy distribution.