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LEGIUS SYNDROME - SPRED1 gene
Clinical Genetic Test
Help
offered by
Clinical Genomics Unit
View lab's test page
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GTR Test Accession: Help GTR000335545.3
INHERITED DISEASEDYSMORPHOLOGYINHERITED DISEASE SUSCEPTIBILITY ... View more
Last updated in GTR: 2019-02-28
View version history
Last annual review date for the lab: 2023-12-01 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation
Conditions (2): Help
Legius syndrome; Neurofibromatosis, type 1
Genes (2): Help
NF1 (17q11.2); SPRED1 (15q14)
Methods (4): Help
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
In cases where it is needed in a clinical diagnostic …
Clinical validity: Help
Not provided
Clinical utility: Help
Establish or confirm diagnosis; Guidance for management; Reproductive decision-making
Ordering Information
Offered by: Help
Clinical Genomics Unit
View lab's website
View lab's test page
Test short name: Help
SPRED1
Manufacturer's name: Help
ICO-IMPPC_HC_Panel_V2.1
Specimen Source: Help
  • Chorionic villi
  • Cord blood
  • Fibroblasts
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Paraffin block
  • Peripheral (whole) blood
  • Skin
  • White blood cell prep
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Physician Assistant
  • Public Health Mandate
Test Order Code: Help
SPRED1 (Complete or Direct)
Lab contact: Help
Elisabeth Castellanos, PhD, Lab Director
ecastellanosp.germanstrias@gencat.cat
+34 930331506
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Result interpretation
Test additional service: Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required: Help
Yes
Test strategy: Help
1)Once we will have the necessary documentation (order form, informed consent and pedigree for familiar cases), the physician / researcher applicant will receive an e-mail confirming the cost of the study to be performed. 2) In case of compliance, the physician / investigator applicant must respond to this e-mail, which … View more
Pre-test genetic counseling required: Help
Yes
Post-test genetic counseling required: Help
Yes
Recommended fields not provided:
How to Order
Conditions Help
Total conditions: 2
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 2
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 4
Method Category Help
Test method Help
Instrument *
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Linkage analysis
SNP Detection
Mutation scanning of select exons
Bi-directional Sanger Sequence Analysis
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation
Clinical utility: Help
Establish or confirm diagnosis
View citations (1)

Guidance for management
View citations (1)

Reproductive decision-making
View citations (1)

Target population: Help
In cases where it is needed in a clinical diagnostic genetic confirmation in patients who meet clinical criteria (complete study) or in cases where the analysis is needed on the presence of a previously identified mutation family (direct study).
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
We follow Clinical Molecular Genetic Society recommendations for the interpretation and reporting of unclassified variants (VUS).

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
Clinical validity, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Procedure: Help
DNA is extracted from a patient's sample. An NGS library is prepared and enriched by capture in solution using our custom hereditary cancer sub-exome target panel (ICO-IMPPC_HC_Panel_V2.0), which include the whole coding regions of NF1 (LRG_214) and SPRED1 (NG_008980.1) genes among others. Enriched library is sequenced in a Illumina platform … View more
Test Confirmation: Help
Mutation is detected DNA level by NGS and validated by an independent technique (Sanger). Splicing mutations that are not previously described are also validated at RNA levels. Studies from patients with mosaicism two independent affected tissues from the same patient are analyzed to detect both first and second hits.
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
95% (n=20)
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
No
VUS:
Software used to interpret novel variations Help
Polyphen, SIFT, PROVEAN, Condel, HSF, NNSplice, SpliceAIDs,
Recommended fields not provided:
Assay limitations, Description of internal test validation method, Citations for Analytical validity, PT Provider, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
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.