Non-NF1 RASopathy NGS Panel
GTR Test Accession: Help GTR000551628.6
INHERITED DISEASEMUSCULOSKELETALCARDIOVASCULAR ... View more
Last updated in GTR: 2023-06-07
Last annual review date for the lab: 2023-06-07 Past due LinkOut
At a Glance
Diagnosis
Noonan syndrome; Cardiofaciocutaneous syndrome 1; Costello syndrome; ...
BRAF (7q34), CBL (11q23.3), HRAS (11p15.5), KRAS (12p12.1), LZTR1 (22q11.21), ...
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Patients with clinical features suggestive of either NS, NSML, CFC, …
Not provided
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Test short name: Help
NNP-NG
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
CPT codes: Help
**AMA CPT codes notice
Lab contact: Help
Bryce Brown, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
ebfincher@uabmc.edu
205-934-5525
Brandon Shaw, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
brandonshaw@uabmc.edu
205-934-1520
Contact Policy: Help
Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.
How to Order: Help
Additional information regarding the specific details needed for test submission can be found on our website
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Result interpretation
Informed consent required: Help
Based on applicable state law
Test strategy: Help
The Non-NF1 Rasopathy panel by NGS involves the simultaneous sequencing of 17 genes: SPRED1, PTPN11, PPP1CB, BRAF, CBL, HRAS, KRAS, LZTR1, NRAS, MAP2K1, MAP2K2, RAF1, RIT1, RASA2, SHOC2, SOS1 and SOS2. The test uses a customized and optimized set of Agilent Haloplex capture probes, followed by sequencing of overlapping amplicons … View more
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Conditions Help
Total conditions: 7
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 17
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Other
Clinical Information
Test purpose: Help
Diagnosis
Target population: Help
Patients with clinical features suggestive of either NS, NSML, CFC, Legius syndrome or Noonan-like syndrome with no mutation previously found by comprehensive RNA-based NF1+/- SPRED1 testing. patients with a clinical diagnosis of any of these syndromes that previously tested negative in a subset of the genes included in this panel; … View more
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
In order to further investigate a VUS, the laboratory will: 1. Review software predictions (SIFT, PolyPhen, etc) 2. Review internal database to compare against alterations seen in >10,000 alleles previously tested in laboratory 3. Offer free of charge family studies for any individuals that would provide useful information for interpretation

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Yes.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
Technical Information
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Analytical sensitivity of next generation sequencing is typically validated using a minimum of 20 DNA samples. No false positives were detected during analysis. The average coverage is >2000x with >98.5% of the coding region ≥350x and 99.3% ≥200x, allowing detection of very low-level mosaicism, down to 3-5% variant allele fraction … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Alternative Assessment
VUS:
Software used to interpret novel variations Help
Alamut, Google search, PolyPhen, SIFT, evolutionary consevation, grantham score, splicing prediction software, disorder specific databases as necessary

Laboratory's policy on reporting novel variations Help
The laboratory will issue an interim report summarizing what is currently known about the variant and familial studies will be offered. Upon completion of the familial studies, a final report will be provided with a conclusion of what is suspected for the alteration.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: Not Applicable
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.