Noonan Spectrum Disorders/RASopathies Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
10327 A2ML1 81479,81479 Order Options and Pricing
BRAF 81406,81479
CBL 81479,81479
HRAS 81404,81479
KRAS 81405,81479
LZTR1 81479,81479
MAP2K1 81406,81479
MAP2K2 81406,81479
MAP3K8 81479,81479
MAPK1 81479,81479
MRAS 81479,81479
NF1 81408,81479
NRAS 81479,81479
PPP1CB 81479,81479
PTPN11 81406,81479
RAF1 81406,81479
RASA2 81479,81479
RIT1 81479,81479
RRAS 81479,81479
RRAS2 81479,81479
SHOC2 81405,81479
SOS1 81406,81479
SOS2 81479,81479
SPRED1 81405,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10327Genes x (24)81442 81404, 81405, 81406, 81408, 81479 $890 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

A 25% additional charge will be applied to STAT orders. View STAT turnaround times here.

For Reflex to PGxome pricing click here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

Turnaround Time

18 days on average

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

The Noonan spectrum disorders, also known as RASopathies, are a group of developmental syndromes characterized by extensive clinical and genetic heterogeneity. They include:

  1. Noonan syndrome
  2. Noonan syndrome with multiple lentigines
  3. Cardiofaciocutaneous syndrome
  4. Costello syndrome

Although there is a considerable phenotypic overlap among the various syndromes, each syndrome is characterized by distinct clinical features.

Noonan syndrome (NS) is characterized by dysmorphic facial features (low-set, posteriorly rotated ears, hypertelorism, downslanted palpebral fissures), short stature, congenital heart defects, and musculoskeletal abnormalities. Cardiac abnormalities are found in up to 80% of patients and most commonly include pulmonary valve stenosis (40%, most common in patients with PTPN11 pathogenic variants) and hypertrophic cardiomyopathy (20%, most common in patients with RIT1 or RAF1 pathogenic variants). Additional cardiac findings can include aortic coarctation, tetralogy of Fallot, septal defects, and mitral valve anomalies. Musculoskeletal abnormalities include short stature, chest deformities (pectus carinatum/pectus excavatum), and short webbed neck. Several additional abnormalities have been described and include lymphatic, hematological, renal, genital, and neurologic findings. Intelligence is usually not affected; however, learning disabilities may be present, but are usually mild. NS is characterized by extensive clinical heterogeneity, even among members of the same family. Diagnosis is often made in infancy or early childhood. Symptoms often change and lessen with advancing age. Infants with NS are at risk of developing juvenile myelomonocytic leukemia (JMML). NS is quite common and has an estimated prevalence of 1 in 1,000-2,500 live births worldwide (Allanson. 1987. PubMed ID: 3543368; Romano et al. 2010. PubMed ID: 20876176; Smpokou et al. 2012. PubMed ID: 23165751; Cao et al. 2017. PubMed ID: 28643916).

Noonan syndrome with multiple lentigines (NSML), previously known as LEOPARD syndrome (multiple Lentigines, Electrocardiographic-conduction abnormalities, Ocular hypertelorism, Pulmonary stenosis, Abnormal genitalia, Retardation of growth, sensorineural Deafness) is characterized by skin pigmentation anomalies including multiple lentigines and café au lait spots, hypertrophic cardiomyopathy, pulmonary valve stenosis, and deafness. Other less common features include short stature, mild mental retardation, and abnormal genitalia (Legius et al. 2002. PubMed ID: 12161596; Sarkozy et al. 2004. PubMed ID: 15121796). The prevalence of NSML is unknown; however, it is likely the second most common RASopathy behind NS.

Cardio-facio-cutaneous syndrome (CFCS) is characterized by congenital heart defects (similar to NS), distinctive facial appearance (broader, longer, and more coarse than NS), and ectodermal abnormalities (sparse brittle hair, hyperkeratotic skin lesions, ichthyosis). Additional features include postnatal growth failure, feeding difficulties with failure to thrive, and neurological findings. Facial features include high forehead; short, upturned nose with a low nasal bridge; prominent external ears that are posteriorly rotated; and ocular hypertelorism. Ectodermal abnormalities are heterogeneous in features and severity. Neurological findings occur in nearly all individuals and include seizures, hypotonia, macrocephaly, developmental delay, and mild to moderate intellectual disability in a majority of individuals (Reynolds et al. 1986. PubMed ID: 3789005). CFCS is very rare and although the exact prevalence is not known, one study in Japan estimated it to be about 1 in 810,000 live births (Abe et al. 2012. PubMed ID: 22495831).

Costello syndrome (CS) is characterized by coarse facial features (macrocephaly, depressed nasal bridge, full lips, large mouth, full cheeks), thick and loose soft skin of the hands and feet, papillomata, congenital heart defects (pulmonary valve stenosis, hypertrophic cardiomyopathy, arrhythmia), increased birth weight followed by postnatal growth retardation, short stature, and developmental delay or mild to moderate intellectual disability is seen in a majority of individuals (van Eeghen et al. 1999. PubMed ID: 9934987; Lin et al. 2002. PubMed ID: 12210337). Patients with CS have an ~15% risk of developing benign and malignant tumors (most commonly rhabdomyosarcoma or neuroblastoma; Gripp et al. 2006. PubMed ID: 16969868). CS is also very rare with estimates of prevalence to be 1 in 380,000-1,290,000 (Giannoulatou et al. 2013. PubMed ID: 24259709; Abe et al. 2012. PubMed ID: 22495831).

Recently, MEK inhibitors have been shown to be successful in treating hypertrophic cardiomyopathy in individuals with pathogenic RIT1 variants (Andelfinger et al. 2019. PubMed ID: 31047013). Determining the genetic etiology of RASopathies may allow for the identification patients eligible for MEK inhibitor treatment, provide a more accurate prognosis, and assess recurrence risk in future pregnancies.

Genetics

Noonan/RASopathy spectrum disorders are caused by dysregulation of the RAS/mitogen-activated protein kinase (Ras/MAPK) signaling pathway, most commonly resulting in the hyperactivation of the RAS/MAPK pathway (Tidyman and Rauen. 2009. PubMed ID: 19467855; Wright and Kerr. 2010. PubMed ID: 20371595; Allanson and Roberts. 2016. PubMed ID: 20301303).

Variants in the following genes have been reported in patients with Noonan spectrum disorders: A2ML1, BRAF, CBL, HRAS, KRAS, LZTR1, MAP2K1, MAP2K2, MAP3K8, MAPK1, MRAS, NF1, NRAS, PPP1CB, PTPN11, RAF1, RASA2, RIT1, RRAS, RRAS2, SHOC2, SOS1, SOS2, and SPRED1. All genes, with one exception, are associated with autosomal dominant inheritance for RASopathy spectrum disorders. LZTR1 is the only exception and has been associated with autosomal dominant and recessive Noonan syndrome.

Multiple genes have limited evidence supporting their association with Noonan-like disorders and include: A2ML1, MAP3K8, and RASA2. For A2ML1, multiple reports have associated variants with RASopathy phenotypes (Justino et al. 2015. PubMed ID: 24896146; van Trier et al. 2015. PubMed ID: 25862627; Vissers et al. 2015. PubMed ID: 24939586; Leung et al. 2018. PubMed ID: 29402968); however, nearly all variants reported are likely too common to be pathogenic, and functional studies were not able to confirm the pathogenicity of any variants that have been tested. A recent paper has challenged the association of A2ML1 and RASopathy spectrum disorders (Brinkmann et al. 2021. PubMed ID: 33082526). To date, only one de novo missense variant in MAP3K8 has been reported, and although functional studies showed both wild type and the missense variant were able to constitutively activate the RAS pathway, there was no difference between the level of activation of wild type and the missense variant (Chen et al. 2014. PubMed ID: 25049390). Three missense variants in RASA2 have been reported in individuals with Noonan syndrome-like phenotypes, and functional studies suggest these variants lead to hyperactivation of the RAS pathway (Chen et al. 2014. PubMed ID: 25049390); however, parental samples were not available to test for disease segregation.

Noonan and Noonan-like syndromes are caused by pathogenic variants in PTPN11, SOS1, RAF1, KRAS, SHOC2, BRAF, NRAS, CBL, RIT1, SOS2, LZTR1, RRAS, MAPK1, MRAS, PPP1CB, RRAS2, NF1, SPRED1, A2ML1, MAP3K8, and RASA2. The majority of pathogenic variants occur in PTPN11 (50%) or SOS1 (10%). RAF1, RIT1, KRAS account for ~5% each with the remaining genes account for <5% individually. The vast majority of pathogenic variants are missense, although a few small deletions, insertions, and indels have been reported, which are all predicted to result in in-frame alterations of the translated protein. Loss-of-function (LOF) variants (nonsense, frameshift, splicing) in many of these genes have been reported previously; however, most are associated with different disorders or are of uncertain significance. LOF PTPN11 variants cause the rare skeletal disorder metachondromatosis (Sobreira et al. 2010. PubMed ID: 20577567). In LZTR1, LOF variants cause recessive NS and dominant schwannomatosis, and in NF1, LOF variants are associated with Noonan syndrome and neurofibromatosis type 1. Copy number variants appear to be an uncommon cause of Noonan and Noonan-like syndromes, with large deletions and duplications being reported in only a few patients with clinical features suggestive of NS (Shchelochkov et al. 2008. PubMed ID: 18348260; Graham et al. 2009. PubMed ID: 19760651; Chen et al. 2014. PubMed ID: 24739123). Although most causative NS pathogenic variants occur de novo, familial cases have been reported. In these families, NS is inherited in an autosomal dominant manner with complete penetrance and variable expressivity (Romano et al. 2010. PubMed ID: 20876176).

NSML, previously known as LEOPARD syndrome, is caused by defects in PTPN11, RAF1, BRAF, MAP2K1, and MAP2K2 (Digilio et al. 2006. PubMed ID: 16733669; Pandit et al. 2007. PubMed ID: 17603483). NSML-causative variants in the PTPN11 gene act through a dominant negative effect, which appears to disrupt the function of the wild-type gene product (SHP2 protein; Kontaridis et al. 2006. PubMed ID: 16377799; Tartaglia et al. 2006. PubMed ID: 16358218). PTPN11 pathogenic variants are the most common cause of NSML and account for ~90% of all cases. Eleven different PTPN11 pathogenic variants, all missense, have been reported in patients with NSML (Human Gene Mutation Database). RAF1, BRAF, MAP2K1, and MAP2K2 pathogenic variants appear to be a rare cause of NSML. De novo pathogenic variants are common; however, familial cases have been reported. In these families, affected relatives are often diagnosed only after the birth of a visibly affected child, and the disease is transmitted in an autosomal dominant manner with variable penetrance and expressivity (Gelb and Tartaglia. 2006. PubMed ID: 16987887).

CFCS is caused by defects in the following RAS/MAPK genes: BRAF, MAP2K1, MAP2K2, KRAS, and NRAS. The vast majority of variants have been reported in BRAF (~75%) or MAP2K1/MAP2K2 (~25%). KRAS and NRAS appear to be rare causes of CFCS. Although most CFCS causative variants are missense, small deletions and duplications have been documented. These are all predicted to result in in-frame alterations of the translated protein. No complex rearrangements have been reported. Nearly all causative variants reported to date occur de novo. Rare cases of inherited pathogenic variants in MAP2K2 and KRAS have been documented (Rauen et al. 2010. PubMed ID: 20358587; Stark et al. 2012. PubMed ID: 21797849).

CS syndrome is caused by pathogenic variants in the HRAS gene (Aoki et al. 2005. PubMed ID: 16170316). Most reported variants are missense and affect codons Gly12 and Gly13. A few indels, which are expected to result in amino acid substitutions, and a 21-bp duplication that is predicted to result in an in-frame duplication of seven residues has been reported in patients with features suggestive of CS (Lorenz et al. 2013. PubMed ID: 23335589; Gripp et al. 2020. PubMed ID: 32499600). Most CS cases are sporadic, resulting from de novo HRAS pathogenic variants.

Somatic mosaicism has been reported for several RAS/MAPK genes. Non-syndromic juvenile myelomonocytic leukemia (JMML) involves somatic PTPN11 pathogenic variants in about 34% of all cases genotyped (Tartaglia et al. 2003. PubMed ID: 12717436). Somatic RAF1 pathogenic variants have been implicated in several human cancers (Pandit et al. 2007. PubMed ID: 17603483; Sarkozy et al. 2009. PubMed ID: 19206169). Somatic KRAS pathogenic variants have also been implicated in several human cancers, including JMML (Reimann et al. 2006. PubMed ID: 16826224) and colon cancer (Edkins et al. 2006. PubMed ID: 16969076). Somatic NRAS pathogenic variants were detected in patients with JMML (Flotho et al. 1999. PubMed ID: 10049057). Somatic recurrent MAP2K1 pathogenic variants have been implicated in several human cancers including melanoma (Nikolaev et al. 2011. PubMed ID: 22197931). Somatic HRAS pathogenic variants have been reported in patients with Costello syndrome (Gripp et al. 2006. PubMed ID: 16329078; Sol-Church et al. 2009. PubMed ID: 19206176).

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

 Gene Noonan Syndrome1 Noonan syndrome with multiple lentigines2 Cardiofaciocutaneous syndrome3 Costello syndrome4
A2ML1 Unknown      
BRAF 0.8% Unknown ~75%  
CBL Unknown      
HRAS       80-90%
KRAS 1.5%   <2%  
LZTR1 2.5%      
MAP2K1   Unknown ~25%  
MAP2K2   Unknown  
MAP3K8 Unknown      
MAPK1 Unknown      
MRAS Unknown      
NF1 Unknown      
NRAS 0.2%   Unknown  
PPP1CB Unknown      
PTPN11 50.0% 90%    
RAF1 5.0% <5%    
RASA2 Unknown      
RIT1 5.0%      
RRAS Unknown      
RRAS2 Unknown      
SHOC2 2.0%      
SOS1 11.0%      
SOS2 1.0%      
SPRED1 Unknown      
  1. Aoki et al. 2016. PubMed ID: 26446362
  2. Gelb and Tartaglia. 2015. PubMed ID: 20301557
  3. Rauen et al. 2016. PubMed ID: 20301365
  4. Gripp and Lin. 2012. PubMed ID: 20301680

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 97.6% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing.

Deletion and duplication testing for NF1 is performed using NGS, but CNVs detected in this gene are usually confirmed via multiplex ligation-dependent probe amplification (MLPA). Please see limitations for CNV detection via NGS.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

Candidates for this RASopathies panel are: patients with clinical features suggestive of Noonan syndrome, cardio-facio-cutaneous syndrome, or Noonan syndrome with multiple lentigines, also known as LEOPARD syndrome; patients with a clinical diagnosis of these syndromes that previously tested negative in a subset of genes included in this panel; patients with a clinical diagnosis of Costello syndrome and no pathogenic variants in HRAS; and patients with Noonan syndrome-like clinical features.

Genes

Official Gene Symbol OMIM ID
A2ML1 610627
BRAF 164757
CBL 165360
HRAS 190020
KRAS 190070
LZTR1 600574
MAP2K1 176872
MAP2K2 601263
MAP3K8 191195
MAPK1 176948
MRAS 608435
NF1 613113
NRAS 164790
PPP1CB 600590
PTPN11 176876
RAF1 164760
RASA2 601589
RIT1 609591
RRAS 165090
RRAS2 600098
SHOC2 602775
SOS1 182530
SOS2 601247
SPRED1 609291
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

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Citations

  • Abe et al. 2012. PubMed ID: 22495831
  • Allanson and Roberts. 2016. PubMed ID: 20301303
  • Allanson. 1987. PubMed ID: 3543368
  • Andelfinger et al. 2019. PubMed ID: 31047013
  • Aoki et al. 2005. PubMed ID: 16170316
  • Aoki et al. 2016. PubMed ID: 26446362
  • Brinkmann et al. 2021. PubMed ID: 33082526
  • Cao et al. 2017. PubMed ID: 28643916
  • Chen et al. 2014. PubMed ID: 24739123
  • Chen et al. 2014. PubMed ID: 25049390
  • Digilio et al. 2006. PubMed ID: 16733669
  • Edkins et al. 2006. PubMed ID: 16969076
  • Flotho et al. 1999. PubMed ID: 10049057
  • Gelb and Tartaglia. 2006. PubMed ID: 16987887
  • Gelb and Tartaglia. 2015. PubMed ID: 20301557
  • Giannoulatou et al. 2013. PubMed ID: 24259709
  • Graham et al. 2009. PubMed ID: 19760651
  • Gripp and Lin. 2012. PubMed ID: 20301680
  • Gripp et al. 2006. PubMed ID: 16329078
  • Gripp et al. 2006. PubMed ID: 16969868
  • Gripp et al. 2020. PubMed ID: 32499600
  • Human Gene Mutation Database (Biobase).
  • Justino et al. 2015. PubMed ID: 24896146
  • Kontaridis et al. 2006. PubMed ID: 16377799
  • Legius et al. 2002. PubMed ID: 12161596
  • Leung et al. 2018. PubMed ID: 29402968
  • Lin et al. 2002. PubMed ID: 12210337
  • Lorenz et al. 2013. PubMed ID: 23335589
  • Nikolaev et al. 2011. PubMed ID: 22197931
  • Pandit et al. 2007. PubMed ID: 17603483
  • Rauen et al. 2010. PubMed ID: 20358587
  • Rauen et al. 2016. PubMed ID: 20301365
  • Reimann et al. 2006. PubMed ID: 16826224
  • Reynolds et al. 1986. PubMed ID: 3789005
  • Romano et al. 2010. PubMed ID: 20876176
  • Sarkozy et al. 2004. PubMed ID: 15121796
  • Sarkozy et al. 2009. PubMed ID: 19206169
  • Shchelochkov et al. 2008. PubMed ID: 18348260
  • Smpokou et al. 2012. PubMed ID: 23165751
  • Sobreira et al. 2010. PubMed ID: 20577567
  • Sol-Church et al. 2009. PubMed ID: 19206176
  • Stark et al. 2012. PubMed ID: 21797849
  • Tartaglia et al. 2003. PubMed ID: 12717436
  • Tartaglia et al. 2006. PubMed ID: 16358218
  • Tidyman and Rauen. 2009. PubMed ID: 19467855
  • van Eeghen et al. 1999. PubMed ID: 9934987
  • van Trier et al. 2015. PubMed ID: 25862627
  • Vissers et al. 2015. PubMed ID: 24939586
  • Wright and Kerr. 2010. PubMed ID: 20371595

Ordering/Specimens

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