GTR Test Accession:
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GTR000597424.1
CAP
Registered in GTR:
2022-03-24
View version history
GTR000597424.1,
registered in GTR:
2022-03-24
Last annual review date for the lab: 2024-05-28
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At a Glance
Test purpose:
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Diagnosis
Conditions (5):
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Genes (5):
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ATXN1 (6p22.3);
ATXN2 (12q24.12);
ATXN3 (14q32.12);
ATXN7 (3p14.1);
CACNA1A (19p13.13)
Methods (1):
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Molecular Genetics - Targeted variant analysis: Trinucleotide repeat by PCR or Southern Blot
Target population: Help
Individuals with clinical features of spinocerebellar ataxia
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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SCAP
Specimen Source:
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- 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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Lab contact:
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Emily Lauer, MS, CGC, 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/overview/609505#Specimen
Order URL
Order URL
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: 5
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 5
| 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
Targeted variant analysis
Trinucleotide repeat by PCR or Southern Blot
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose:
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Diagnosis
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Spinocerebellar ataxias. Soong BW, et al. Handb Clin Neurol. 2018;155:143-174. doi:10.1016/B978-0-444-64189-2.00010-X. PMID: 29891056.
Target population:
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Individuals with clinical features of spinocerebellar ataxia
View citations (1)
- Spinocerebellar ataxias. Soong BW, et al. Handb Clin Neurol. 2018;155:143-174. doi:10.1016/B978-0-444-64189-2.00010-X. PMID: 29891056.
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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Decline to answer. Contact lab for details
Decline to answer. 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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A polymerase-chain reaction-based assay is used to amplify across the region of the ATXN1, ATXN2, ATXN3, CACNA1A, or ATXN7 genes containing CAG repeats. Additionally, testing assesses for CAT trinucleotides that interrupt the CAG repeat tract within the ATXN1 gene.(Unpublished Mayo method)
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Analytical sensitivity, specificity, and accuracy are ≥ 99%
Assay limitations:
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For predictive testing, it is important to first document the presence of a cytosine-adenine-guanine (CAG)-repeat expansion in an affected family member to confirm that the repeat expansion is the underlying mechanism of disease in the family. It is strongly recommended that patients undergoing predictive testing receive genetic counseling both prior …
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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
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
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:
Test Confirmation,
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:
Molecular resources:
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.