GTR Test Accession:
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GTR000500351.3
CAP
Last updated in GTR: 2020-08-10
View version history
GTR000500351.3, last updated: 2020-08-10
GTR000500351.2, last updated: 2019-08-13
GTR000500351.1, last updated: 2018-08-20
Last annual review date for the lab: 2023-07-18
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At a Glance
Test purpose:
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Diagnosis;
Monitoring;
Mutation Confirmation; ...
Conditions (1):
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Agenesis of the corpus callosum with peripheral neuropathy
Genes (1):
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SLC12A6 (15q14)
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
The target population for this test is patients suspected of …
Clinical validity:
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Mutations of the SLC12A6 [OMIM #604878] gene have been identified …
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Specimen Source:
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- Amniocytes
- Amniotic fluid
- Buccal swab
- Cell culture
- Chorionic villi
- Cord blood
- Fetal blood
- Fibroblasts
- Fresh tissue
- Frozen tissue
- Peripheral (whole) blood
- Product of conception (POC)
- Saliva
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Registered Nurse
CPT codes:
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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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All samples should be shipped via overnight delivery at room temperature.
No weekend or holiday deliveries.
Label each specimen with the patient’s name, date of birth and date sample collected.
Send specimens with complete requisition and consent form, otherwise, specimen processing may be delayed.
Order URL
No weekend or holiday deliveries.
Label each specimen with the patient’s name, date of birth and date sample collected.
Send specimens with complete requisition and consent form, otherwise, specimen processing may be delayed.
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Confirmation of research findings
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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Decline to answer
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:
Test Order Code,
Lab contact for this test,
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: 2
Method Category
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Test method
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Instrument *
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose:
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Diagnosis;
Monitoring;
Mutation Confirmation;
Pre-symptomatic;
Risk Assessment;
Screening
Clinical validity:
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Mutations of the SLC12A6 [OMIM #604878] gene have been identified in patients with HMSN/ACC. SLC12A6 has 25 coding exons and is located at 15q14. SLC12A6 encodes the potassium-chloride cotransporter KCC3 and is highly expressed in the brain. A founder mutation (c.2436delG) in exon 18 is identified in almost all patients …
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View citations (1)
- Howard HC, Mount DB, Rochefort D, Byun N, Dupré N, Lu J, Fan X, Song L, Rivière JB, Prévost C, Horst J, Simonati A, Lemcke B, Welch R, England R, Zhan FQ, Mercado A, Siesser WB, George AL, McDonald MP, Bouchard JP, Mathieu J, Delpire E, Rouleau GA. The K-Cl cotransporter KCC3 is mutant in a severe peripheral neuropathy associated with agenesis of the corpus callosum. Nat Genet. 2002;32(3):384-92. doi:10.1038/ng1002. Epub 2002 Oct 07. PMID: 12368912.
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Howard HC, Mount DB, Rochefort D, Byun N, Dupré N, Lu J, Fan X, Song L, Rivière JB, Prévost C, Horst J, Simonati A, Lemcke B, Welch R, England R, Zhan FQ, Mercado A, Siesser WB, George AL, McDonald MP, Bouchard JP, Mathieu J, Delpire E, Rouleau GA. The K-Cl cotransporter KCC3 is mutant in a severe peripheral neuropathy associated with agenesis of the corpus callosum. Nat Genet. 2002;32(3):384-92. doi:10.1038/ng1002. Epub 2002 Oct 07. PMID: 12368912.
Target population:
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The target population for this test is patients suspected of having Hereditary Motor and Sensory Neuropathy with Agenesis of the Corpus Callosum
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Variants are identified and evaluated using a custom collection of bioinformatic tools and comprehensively interpreted by our team of directors and genetic counselors.
Variants are identified and evaluated using a custom collection of bioinformatic tools and comprehensively interpreted by our team of directors and genetic counselors.
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Decline to answer.
Decline to answer.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes.
Yes.
Research:
Is research allowed on the sample after clinical testing is complete?
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http://dnatesting.uchicago.edu/research-consent-form
http://dnatesting.uchicago.edu/research-consent-form
Recommended fields not provided:
Sample negative report,
Sample positive report
Technical Information
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%
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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A custom collection of bioinformatics tools
Laboratory's policy on reporting novel variations Help
All novel and/or potentially pathogenic variants are confirmed by Sanger sequencing
A custom collection of bioinformatics tools
Laboratory's policy on reporting novel variations Help
All novel and/or potentially pathogenic variants are confirmed by Sanger sequencing
Recommended fields not provided:
Test Confirmation,
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:
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Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.