GTR Test Accession:
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GTR000561371.1
Last updated in GTR: 2018-07-19
View version history
GTR000561371.1, last updated: 2018-07-19
Last annual review date for the lab: 2020-11-04
Past due
LinkOut
At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation
Conditions (1):
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Primary hyperoxaluria, type I
Genes (1):
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AGXT (2q37.3)
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Uni-directional Sanger sequencing
Target population: Help
Patients with hyperoxaluria, nephrocalcinosis, calcium oxalate renal stone disease and …
Clinical validity:
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Not provided
Clinical utility:
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Not provided
Ordering Information
Offered by:
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Test short name:
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PH Type 1
Specimen Source:
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- Chorionic villi
- Isolated DNA
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
Test Order Code:
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Primary Hyperoxaluria Type 1
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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Please visit lab website for details and contact lab before sending; emma.walker15@nhs.net.
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Custom Sequence Analysis
Result interpretation
Custom Sequence Analysis
Result interpretation
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Yes
Test strategy:
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PH1 step 1: Sequencing of exons 1 and 4 which contain common mutations c.33dupC and c.508A (Gly170Arg). This screen has a test sensitivity of 75% and a diagnostic sensitivity of 50%.
PH1 step 2: Sequencing of remaining exons of the gene.
PH1 step 2: Sequencing of remaining exons of the gene.
View citations (1)
- Williams E, Rumsby G. Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. Clin Chem. 2007;53(7):1216-21. doi:10.1373/clinchem.2006.084434. Epub 2007 May 10. PMID: 17495019.
Pre-test genetic counseling required:
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No
Post-test genetic counseling required:
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No
Recommended fields not provided:
Lab contact for this test
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
Uni-directional Sanger sequencing
Applied Biosystems Seq Studio genetic analyser
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation
Target population:
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Patients with hyperoxaluria, nephrocalcinosis, calcium oxalate renal stone disease and ESRD.
View citations (1)
- Milliner DS, Harris PC, Sas DJ, Cogal AG, Lieske JC. Primary Hyperoxaluria Type 1. 2002 Jun 19 [updated 2022 Feb 10]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. PMID: 20301460.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Linkage is confirmed by analysis of parental DNA samples. Novel variants and VUS undergo in silico analysis with prediction software and are interpreted in accordance with the practice guidelines of the UK Association for Clinical Molecular Genetics.
Linkage is confirmed by analysis of parental DNA samples. Novel variants and VUS undergo in silico analysis with prediction software and are interpreted in accordance with the practice guidelines of the UK Association for Clinical Molecular Genetics.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Not provided. We do not routinely re-contact the ordering physician if the variant interpretation changes as new information becomes available.
Not provided. We do not routinely re-contact the ordering physician if the variant interpretation changes as new information becomes available.
Sample reports:
Sample Negative Report
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Sample Negative Report
Sample Positive Report Help
Sample Positive Report
Sample VUS Report Help
Sample VUS Report
Sample Negative Report
Sample Positive Report Help
Sample Positive Report
Sample VUS Report Help
Sample VUS Report
Recommended fields not provided:
Clinical validity,
Clinical utility,
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Will the lab re-contact the ordering physician if variant interpretation changes?,
Is research allowed on the sample after clinical testing is complete?
Technical Information
Test Procedure:
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Sanger sequencing of coding exons of the gene and 20-50 bp of the 5' and 3' flanking intronic regions.
View citations (1)
- Williams E, Rumsby G. Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. Clin Chem. 2007;53(7):1216-21. doi:10.1373/clinchem.2006.084434. Epub 2007 May 10. PMID: 17495019.
Test Platform:
Applied Biosystems Seq Studio genetic analyser
Availability:
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Tests performed
Interpretation performed in-house
Report generated in-house
Specimen preparation performed in-house
Wet lab work performed in-house
Interpretation performed in-house
Report generated in-house
Specimen preparation performed in-house
Wet lab work performed in-house
Analytical Validity:
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Whole gene analysis was performed on genomic DNA samples from 300 biopsy proven patients with Primary Hyperoxaluria type 1.
The diagnostic sensitivity of this test was shown to be 98%.
View citations (1)
- Williams E, Rumsby G. Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. Clin Chem. 2007;53(7):1216-21. doi:10.1373/clinchem.2006.084434. Epub 2007 May 10. PMID: 17495019.
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
European Molecular Genetics Quality Network, EMQN
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
European Molecular Genetics Quality Network, EMQN
VUS:
Software used to interpret novel variations
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SIFT, PolyPhen2, Mutation taster
Laboratory's policy on reporting novel variations Help
Reported with interpretation based upon prediction software and advice on further biochemical testing which may assist in establishing a diagnosis.
SIFT, PolyPhen2, Mutation taster
Laboratory's policy on reporting novel variations Help
Reported with interpretation based upon prediction software and advice on further biochemical testing which may assist in establishing a diagnosis.
Recommended fields not provided:
Test Confirmation,
Assay limitations,
Description of internal test validation method,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
Not Applicable
Additional Information
Clinical resources:
Molecular 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.