GTR Test Accession:
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GTR000548230.2
Last updated in GTR:
2023-01-16
View version history
GTR000548230.2,
last updated:
2023-01-16
GTR000548230.1,
registered in GTR:
2021-03-03
Last annual review date for the lab: 2023-01-17
Past due
LinkOut
At a Glance
Test purpose:
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Diagnosis;
Drug Response;
Monitoring; ...
Conditions (1):
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Developmental and epileptic encephalopathy, 14
Genes (1):
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KCNT1 (9q34.3)
Methods (2):
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Molecular Genetics - Sequence analysis of select exons: Bi-directional Sanger Sequence Analysis; ...
Target population: Help
Any
Clinical validity:
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Not provided
Clinical utility:
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Not provided
Ordering Information
Offered by:
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Specimen Source:
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- Amniotic fluid
- Buffy coat
- Chorionic villi
- Isolated DNA
- Paraffin block
- Peripheral (whole) blood
- Saliva
- White blood cell prep
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
Test Order Code:
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KCNT1
How to Order:
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Together with the filled-in requeistion form forward 2ml of EDTA stabilized peripheral blood or 2 ug of standard purified DNA
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Confirmation of research findings
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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Yes
Post-test genetic counseling required:
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Yes
Recommended fields not provided:
Lab contact for this test,
Contact policy,
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
Sequence analysis of select exons
Bi-directional Sanger Sequence Analysis
SMDX9614
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Iontorrent PGM
Clinical Information
Test purpose:
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Diagnosis;
Drug Response;
Monitoring;
Mutation Confirmation;
Pre-symptomatic;
Predictive;
Prognostic;
Risk Assessment;
Screening
Target population:
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Any
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Use gene specific databases, HGMD, PubMed
Use gene specific databases, HGMD, PubMed
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Yes.
Yes.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes. Whenever the status of a genetic variation is changed we will contact the requesting professional if he/she is not available the department will be contacted
Yes. Whenever the status of a genetic variation is changed we will contact the requesting professional if he/she is not available the department will be contacted
Research:
Is research allowed on the sample after clinical testing is complete?
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None
None
Recommended fields not provided:
Clinical validity,
Clinical utility,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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Sanger sequencing
Test Confirmation:
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Sanger sequencing
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Accuracy 99%, Sensivity 99%, Specificity 100%, Precision 99%
Assay limitations:
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Contaminated DNA, impure DNA, limited sample amount.
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
Description of PT method: Help
Proficiency is validated as part of the general lab validation of the protocols for NGS and Sanger sequencing
Description of internal test validation method: Help
Coverage of entire target region, reading depth of at least x30, Phred score at a minimum of Q 20-30
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
European Molecular Genetics Quality Network, EMQN
Description of PT method: Help
Proficiency is validated as part of the general lab validation of the protocols for NGS and Sanger sequencing
Description of internal test validation method: Help
Coverage of entire target region, reading depth of at least x30, Phred score at a minimum of Q 20-30
VUS:
Software used to interpret novel variations
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PolyPhen, SIFT, AGVGD, Mutationtaster, Mutationaccessor, SpliceSiteFinder, GeneSplicer
Laboratory's policy on reporting novel variations Help
The noval variant will be reported to the requesting professional. Reporting to any other facility depends on the requesting professional.
PolyPhen, SIFT, AGVGD, Mutationtaster, Mutationaccessor, SpliceSiteFinder, GeneSplicer
Laboratory's policy on reporting novel variations Help
The noval variant will be reported to the requesting professional. Reporting to any other facility depends on the requesting professional.
Recommended fields not provided:
Citations to support assay limitations,
Citations to support internal test validation method,
Citations for Analytical validity,
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:
Consumer 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.