GTR Test Accession:
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GTR000593145.1
Last updated in GTR: 2021-05-24
View version history
GTR000593145.1, last updated: 2021-05-24
Last annual review date for the lab: 2024-05-28
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic; ...
Conditions (1):
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Spinal muscular atrophy
Genes (1):
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SMN1 (5q13.2)
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis
Target population: Help
Individuals with clinical features of Spinal Muscular Atrophy.
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Test short name:
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SMN1Z
Specimen Source:
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- Dried blood spot (DBS) card
- Fibroblasts
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Dentist
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Public Health Mandate
- Registered Nurse
Test Order Code:
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SMN1Z
View other test codes
View other test codes
Lab contact:
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Huong Cabral, MS, Certified Genetic counselor, CGC, Genetic Counselor
GCMolgen@mayo.edu
1-800-533-1710
GCMolgen@mayo.edu
1-800-533-1710
Contact Policy:
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Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order:
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https://www.mayocliniclabs.com/test-catalog/Specimen/65941
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Comment: FMTT
OrderCode: FMTT
Comment: FMTT
OrderCode: FMTT
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Based on applicable state law
Pre-test genetic counseling required:
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No
Post-test genetic counseling required:
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No
Recommended fields not provided:
Test strategy
Conditions
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Total conditions: 1
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 1
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
Methodology
Total methods: 1
Method Category
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Test method
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Instrument
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
ABI 3730xl DNA Analyzer
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic;
Predictive;
Prognostic;
Recurrence;
Risk Assessment;
Screening
Clinical utility:
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Establish or confirm diagnosis
Target population:
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Individuals with clinical features of Spinal Muscular Atrophy.
View citations (1)
- An update of the mutation spectrum of the survival motor neuron gene (SMN1) in autosomal recessive spinal muscular atrophy (SMA). Wirth B, et al. Hum Mutat. 2000;15(3):228-37. doi:10.1002/(SICI)1098-1004(200003)15:3<228::AID-HUMU3>3.0.CO;2-9. PMID: 10679938.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Yes. Contact lab for details
Yes. Contact lab for details
Will the lab re-contact the ordering physician if variant interpretation changes?
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No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
Research:
Is research allowed on the sample after clinical testing is complete?
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Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Recommended fields not provided:
Clinical validity,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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Long-range-PCR of SMN1 exons 2-8, followed by bidirectional Sanger sequence analysis for nucleotide variants in all protein-coding regions and intron/exon boundaries of SMN1. SMN1 exon 1 is PCR-amplified and bidirectionally Sanger-sequenced.(Unpublished Mayo method)
Test Confirmation:
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Positive results are confirmed when appropriate
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Sequence analysis has an analytical sensitivity of approximately 99% for nucleotide base alterations, small deletions, and insertions. Low-level mosaicism will not be detected by routine sequencing methodologies.
Assay limitations:
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Variants detected in SMN1 exon 1 cannot be distinguished from variants inSMN2 exon 1. Therefore, additional molecular analyses are required to confirm results in this region. A small percentage of individuals who are carriers or have a diagnosis of spinal muscular atrophy may have a variant that is not identified …
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Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Platform PT performed
PT Provider: Help
Platform PT performed
Yes
Method used for proficiency testing: Help
Platform PT performed
PT Provider: Help
Platform PT performed
VUS:
Software used to interpret novel variations
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Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel variants and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel variants and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Recommended fields not provided:
Citations to support assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Clinical resources:
Practice guidelines:
Consumer resources:
IMPORTANT NOTE:
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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.