Neurofibromatosis (NF) Type 1 and Legius Syndrome Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
10099 NF1 81408,81479 Order Options and Pricing
SPRED1 81405,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10099Genes x (2)81479 81405(x1), 81408(x1), 81479(x2) $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 Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

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

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Brett Deml, PhD

Clinical Features and Genetics

Clinical Features

Neurofibromatosis type 1 (NF1) is characterized by cutaneous neurofibromas, café-au-lait macules (CALMs), iris hamartoma (Lisch nodules) and freckling of axillary and inguinal regions. These features usually become apparent during puberty. Additional features include plexiform neurofibromas, central nervous system gliomas, including optic glioma, macrocephaly, scoliosis, pseudoarthritis, overgrowth and learning difficulties (Riccardi 1993). There is extensive clinical variability between individuals in age of onset, tumor burden, and disease progression. NF1 is pan-ethnic and affects 1 in 3,000 people (Rasmussen and Friedman 2000).

Neurofibromatosis-Noonan Syndrome patients (NFNS) present with clinical features characteristic of both neurofibromatosis type 1 (NF1) and Noonan syndrome (NS). The NF1 features include CALMs, freckling, neurofibromas, hamartoma of the iris, optic gliomas, and other MRI findings, such as unidentified bright objects (UBO). The NS features include facial anomalies such as hypertelorism, low-set ears, short stature, congenital heart defects, primary pulmonary valve stenosis, webbed neck and thoracic abnormalities. In NFNS patients, features common to both NF1 and NS include macrocephaly, scoliosis, mental retardation or learning difficulties (Allanson et al.1985; De Luca et al. 2005). Spinal Neurofibromatosis (SNF) is characterized by multiple bilateral spinal neurofibromas and other tumors of the central nervous system, with few or no other clinical features of NF1. Symptoms usually begin in adulthood (Kluwe et al. 2003; Quintáns et al. 2011).

Legius Syndrome, previously known as neurofibromatosis type 1-like syndrome, is a developmental disorder characterized by a mild NF1 phenotype (Brems et al. 2007; Stowe et al. 2012). The most common clinical features of Legius syndrome are multiple café-au-lait spots. Additional features may include a Noonan-like dysmorphy, axillary freckling, macrocephaly, psychomotor developmental delay, behavioral problems and learning difficulties. Although Legius syndrome resembles the Neurofibromatosis Type 1 phenotype, some typical features of NF1, such as Lisch nodules in the iris, neurofibromas and central nervous system tumors are absent (Brems et al. 2007).

Genetics

Neurofibromatosis type 1 is caused by heterozygous loss-of-function pathogenic variants in the NF1 gene. It is inherited as an autosomal dominant trait in about half of cases, and is caused by de novo pathogenic variants in the other half. Over 2,300 NF1 germline variants have been reported and include all types. Large deletions account for ~ 5% of patients with NF1 and are usually associated with a severe phenotype (Friedman 2014). Gross insertions and complex rearrangements are rare. Nearly all de novo pathogenic variants occur in the paternal chromosomes (Jadayel et al. 1990), with the exception of large deletions, which occur in maternal chromosomes (Lázaro et al. 1996; Upadhyaya et al. 1998). Parental germline mosaicism has been reported (Lázaro et al. 1994).

The vast majority of NFNS cases are sporadic, although several families transmitting the trait in an autosomal dominant manner have been reported (Quattrin et al. 1987; Abuelo et al. 1988; Colley et al. 1996). Heterozygous mutations in the NF1 gene were reported in patients with NFNS, including sporadic and familial cases (Baralle et al. 2003; De Luca et al. 2005; Stevenson et al. 2006; Huffmeier et al. 2006). At least 10 different pathogenic variants in the NF1 gene were detected in patients with NFNS. About half of these are missense, the other half are small deletions or insertions that are predicted to result either in frameshift or in-frame deletions.

NF1 encodes the neurofibromin protein, a negative regulator of the RAS/MAPK pathway.

Legius syndrome is inherited in an autosomal dominant manner in most reported cases; while family medical history was not available for several patients. It is therefore not clear whether these cases are familial or sporadic. Heterozygous germline loss-of function pathogenic variants in the SPRED1 gene cause Legius syndrome. Over 70 SPRED1 pathogenic variants have been reported to date. They are distributed throughout the gene and are mostly truncating (Spencer et al. 2011).

The SPRED1 protein negatively regulates MAP kinase signaling within the RAS-MAPK pathway. It interacts with neurofibromin.

Clinical Sensitivity - Sequencing with CNV PGxome

This panel will detect pathogenic variants in the:

- NF1 gene in 80-93% of patients that meet the NIH clinical diagnostic criteria for neurofibromatosis type 1 (Maruoka et al. 2014; van Minkelen et al. 2014; Pasmant et al. 2015; Zhang et al. 2015; Calì et al. 2017).

- SPRED1 gene in ~ 2 % of patients with NIH clinical diagnostic criteria for neurofibromatosis type 1 and no pathogenic variants in the NF1 gene (Messiaen et al. 2009).

- SPRED1 gene in ~ 10% of patients with Legius syndrome (mild neurofibromatosis type 1 phenotype) (Brems et al. 2012; Spurlock et al. 2009).

Deletions and duplications of NF1 represent ~5% of cases (Friedman 2014).

Large copy number variations in the genomic region of the SPRED1 gene are found in ~ 5% of patients with Legius syndrome (mild neurofibromatosis type 1 phenotype) (Brems et al. 2012).

Testing Strategy

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

This panel provides 100% 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. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

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.

Indications for Test

Clinical features of neurofibromatosis type1 overlap with those of Legius syndrome. Candidates for this panel are: patients with clinical features of NF1, NFNS, SNF, or Legius syndrome. All patients with CALMs and no other clinical manifestations are also candidates for this panel (Bianchi et al. 2015; Benelli et al. 2015).

Genes

Official Gene Symbol OMIM ID
NF1 613113
SPRED1 609291
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
PGxome®

Citations

  • Abuelo D.N., Meryash D.L. 1988. American Journal of Medical Genetics. 29: 937-41. PubMed ID: 3135755
  • Allanson J.E. et al. 1985. American Journal of Medical Genetics. 21: 457-62. PubMed ID: 2411134
  • Baralle D. et al. 2003. American Journal of Medical Genetics. Part A. 119A: 1-8. PubMed ID: 12707950
  • Benelli E. et al. 2015. Italian Journal of Pediatrics. 41: 8. PubMed ID: 25883013
  • Bianchi M. et al. 2015. Human Genome Variation. 2: 15051. PubMed ID: 27081556
  • Brems H. et al. 2007. Nature Genetics. 39: 1120-6. PubMed ID: 17704776
  • Brems H. et al. 2012. Human Mutation. 33: 1538-46. PubMed ID: 22753041
  • Calì et al. 2017. PubMed ID: 27838393)
  • Colley A. et al. 1996. Clinical Genetics. 49: 59-64. PubMed ID: 8740913
  • De Luca A. et al. 2005. American Journal of Human Genetics. 77: 1092-101. PubMed ID: 16380919
  • Friedman J. 2014. Neurofibromatosis 1. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301288
  • Hüffmeier U. et al. 2006. American Journal of Medical Genetics. Part A. 140: 2749-56. PubMed ID: 17103458
  • Jadayel D. et al. 1990. Nature. 343: 558-9. PubMed ID: 2105472
  • Kluwe L. et al. 2003. Journal of Medical Genetics. 40: 368-71. PubMed ID: 12746402
  • Lázaro C. et al. 1994. The New England Journal of Medicine. 331: 1403-7. PubMed ID: 7969279
  • Lázaro C. et al. 1996. Human Genetics. 98: 696-9. PubMed ID: 8931703
  • Maruoka et al. 2014. PubMed ID: 25325900
  • Messiaen L. et al. 2009. JAMA. 302: 2111-8. PubMed ID: 19920235
  • Pasmant et al. 2015. PubMed ID: 25074460
  • Quattrin T. et al. 1987. American Journal of Medical Genetics. 26: 645-9. PubMed ID: 3105315
  • Quintáns B. et al. 2011. Case Reports in Neurology. 3: 86-90. PubMed ID: 21532985
  • Rasmussen S.A., Friedman J.M. 2000. American Journal of Epidemiology. 151: 33-40. PubMed ID: 10625171
  • Riccardi V.M. 1993. American Journal of Human Genetics. 53: 301-4. PubMed ID: 8328448
  • Spencer E. et al. 2011. American Journal of Medical Genetics. Part A. 155A: 1352-9. PubMed ID: 21548021
  • Spurlock G. et al. 2009. Journal of Medical Genetics. 46: 431-7. PubMed ID: 19443465
  • Stevenson D.A. et al. 2006. Clinical Genetics. 69: 246-53. PubMed ID: 16542390
  • Stowe I.B. et al. 2012. Genes & Development. 26: 1421-6. PubMed ID: 22751498
  • Upadhyaya M. et al. 1998. Human Genetics. 102: 591-7. PubMed ID: 9654211
  • van Minkelen et al. 2014. PubMed ID: 23656349
  • Zhang et al. 2015. PubMed ID: 26056819

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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