GTR Test Accession:
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GTR000506901.1
Last updated in GTR: 2013-08-22
View version history
GTR000506901.1, last updated: 2013-08-22
Last annual review date for the lab: 2023-06-16
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Risk Assessment; ...
Conditions (1):
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Lysinuric protein intolerance
Genes (1):
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SLC7A7 (14q11.2)
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis
Target population: Help
Patients with a diagnosis of Lysinuric protein intolerance.
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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Specimen Source:
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- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
Test Order Code:
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SLC7A
View other test codes
View other test codes
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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Provide appropriate sample, relevant clinical information and a completed requisition form.
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Sequence Analysis
Confirmation of research findings
Custom Sequence Analysis
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Decline to answer
Test strategy:
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http://www.pathology.med.umich.edu/handbook/
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Recommended fields not provided:
Lab contact for this test
Conditions
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Total conditions: 1
Condition/Phenotype | Identifier |
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Test Targets
Genes
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Total genes: 1
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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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
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Risk Assessment;
Screening
Clinical utility:
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Establish or confirm diagnosis
Target population:
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Patients with a diagnosis of Lysinuric protein intolerance.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Follow ACMG guidelines, suggest family study
Follow ACMG guidelines, suggest family study
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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No.
No.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes. by Phone or secure email
Yes. by Phone or secure email
Recommended fields not provided:
Clinical validity,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Confirmation:
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Using new sample
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 99-100% Accuracy 100% Precision 100%
Assay limitations:
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Does not detect large deletions, duplications and rearrangement in the SLC7A7 gene region. It does not detect promoter or deep intronic mutations.
Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Intra-Laboratory
Yes
Method used for proficiency testing: Help
Intra-Laboratory
VUS:
Software used to interpret novel variations
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SIFT, PolyPhen2, RESCUE-ESE Web Server, Berkeley Drosophila Genome Project
Laboratory's policy on reporting novel variations Help
Contact ordering physician by phone and by routine report; recommend clinical genetics follow up and/or genetic counseling and parental testing
SIFT, PolyPhen2, RESCUE-ESE Web Server, Berkeley Drosophila Genome Project
Laboratory's policy on reporting novel variations Help
Contact ordering physician by phone and by routine report; recommend clinical genetics follow up and/or genetic counseling and parental testing
Recommended fields not provided:
Citations to support 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:
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Category:
FDA exercises enforcement discretion
Additional Information
Clinical resources:
Molecular resources:
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Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.