Clinical Genetic Test
offered by
GTR Test Accession:
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GTR000282123.1
Registered in GTR:
2013-05-24
View version history
GTR000282123.1,
registered in GTR:
2013-05-24
Last annual review date for the lab: 2024-05-10
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic
Conditions (2):
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Renal coloboma syndrome;
Renal hypoplasia
Genes (1):
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PAX2 (10q24.31)
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)
Target population: Help
Individuals with suspected renal coloboma syndrome (RCS); family members of …
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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- Amniotic fluid
- Chorionic villi
- Isolated DNA
- Peripheral (whole) blood
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Dentist
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Registered Nurse
Test Order Code:
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PAX2
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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Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
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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Based on applicable state law
Test strategy:
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Sequencing of coding region and intron/exon boundaries.
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: 2
| 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
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina HiSeq™2000 system
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Bower M, Salomon R, Allanson J, Antignac C, Benedicenti F, Benetti E, Binenbaum G, Jensen UB, Cochat P, DeCramer S, Dixon J, Drouin R, Falk MJ, Feret H, Gise R, Hunter A, Johnson K, Kumar R, Lavocat MP, Martin L, Morinière V, Mowat D, Murer L, Nguyen HT, Peretz-Amit G, Pierce E, Place E, Rodig N, Salerno A, Sastry S, Sato T, Sayer JA, Schaafsma GC, Shoemaker L, Stockton DW, Tan WH, Tenconi R, Vanhille P, Vats A, Wang X, Warman B, Weleber RG, White SM, Wilson-Brackett C, Zand DJ, Eccles M, Schimmenti LA, Heidet L. Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database. Hum Mutat. 2012;33(3):457-66. doi:10.1002/humu.22020. Epub 2012 Jan 31. PMID: 22213154.
Target population:
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Individuals with suspected renal coloboma syndrome (RCS); family members of individuals with RCS.
View citations (1)
- Bower M, Salomon R, Allanson J, Antignac C, Benedicenti F, Benetti E, Binenbaum G, Jensen UB, Cochat P, DeCramer S, Dixon J, Drouin R, Falk MJ, Feret H, Gise R, Hunter A, Johnson K, Kumar R, Lavocat MP, Martin L, Morinière V, Mowat D, Murer L, Nguyen HT, Peretz-Amit G, Pierce E, Place E, Rodig N, Salerno A, Sastry S, Sato T, Sayer JA, Schaafsma GC, Shoemaker L, Stockton DW, Tan WH, Tenconi R, Vanhille P, Vats A, Wang X, Warman B, Weleber RG, White SM, Wilson-Brackett C, Zand DJ, Eccles M, Schimmenti LA, Heidet L. Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database. Hum Mutat. 2012;33(3):457-66. doi:10.1002/humu.22020. Epub 2012 Jan 31. PMID: 22213154.
Variant Interpretation:
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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Not provided.
Not provided.
Research:
Is research allowed on the sample after clinical testing is complete?
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Test development & QC. Patients can consent to be part of registry used to submit data to LSDB.
Test development & QC. Patients can consent to be part of registry used to submit data to LSDB.
Recommended fields not provided:
Clinical validity,
What is the protocol for interpreting a variation as a VUS?,
Will the lab re-contact the ordering physician if variant interpretation changes?,
Sample negative report,
Sample positive report
Technical Information
Availability:
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Tests performed
Interpretation performed in-house
Report generated in-house
Specimen preparation performed in-house
Wet lab work performed at an outside lab
Test performance comments
Sequencing performed at separate on-site facility with a different CLIA certification
Interpretation performed in-house
Report generated in-house
Specimen preparation performed in-house
Wet lab work performed at an outside lab
Test performance comments
Sequencing performed at separate on-site facility with a different CLIA certification
Analytical Validity:
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Will detect >95% of mutations associated with RCS. Will detect causative mutations in >99% of individuals with PAX2-related RCS.
View citations (1)
- www.lovd.nl/PAX2
Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Inter-Laboratory
Yes
Method used for proficiency testing: Help
Inter-Laboratory
VUS:
Laboratory's policy on reporting novel variations
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Novel variations are reported and family studies recommended.
Novel variations are reported and family studies recommended.
Recommended fields not provided:
Test Confirmation,
Assay limitations,
Description of internal test validation method,
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:
Practice guidelines:
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.