GTR Test Accession:
Help
GTR000254580.2
CAP
Last updated in GTR: 2012-09-27
View version history
GTR000254580.2, last updated: 2012-09-27
GTR000254580.1, last updated: 2013-11-15
Last annual review date for the lab: 2022-10-27
Past due
LinkOut
At a Glance
Test purpose:
Help
Diagnosis
Conditions (1):
Help
Muscle eye brain disease
Genes (1):
Help
POMGNT1 (1p34.1)
Methods (2):
Help
Biochemical Genetics - Enzyme assay: Enzymatic levels; ...
Target population: Help
Not provided
Clinical validity:
Help
Not provided
Clinical utility:
Help
Not provided
Ordering Information
Offered by:
Help
Specimen Source:
Help
- Amniocytes
- Chorionic villi
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Health Care Provider
Lab contact:
Help
Contact Policy:
Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
Test service:
Help
Clinical Testing/Confirmation of Mutations Identified Previously
Test additional service:
Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Test development:
Help
Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required:
Help
Decline to answer
Pre-test genetic counseling required:
Help
Decline to answer
Post-test genetic counseling required:
Help
Decline to answer
Recommended fields not provided:
Test Order Code,
How to Order,
Test strategy
Conditions
Help
Total conditions: 1
Condition/Phenotype | Identifier |
---|
Test Targets
Genes
Help
Total genes: 1
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
---|
Methodology
Total methods: 2
Method Category
Help
Test method
Help
Instrument *
Enzyme assay
Enzymatic levels
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
* Instrument: Not provided
Clinical Information
Test purpose:
Help
Diagnosis
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
Help
Novel variations are evaluated using a variety of algorithms including splice site analysis, sequence conservation within species and isoforms and functional estimation (i.e. SIFT, Polyphen, AlignGVGD & Mutation Taster). If the variation cannot be placed into a pathogenic or non-pathogenic state, further studies including evaluation of family members and/or assessing … View more
Novel variations are evaluated using a variety of algorithms including splice site analysis, sequence conservation within species and isoforms and functional estimation (i.e. SIFT, Polyphen, AlignGVGD & Mutation Taster). If the variation cannot be placed into a pathogenic or non-pathogenic state, further studies including evaluation of family members and/or assessing … View more
Are family members with defined clinical status recruited to assess significance of VUS without charge?
Help
Yes.
Yes.
Will the lab re-contact the ordering physician if variant interpretation changes?
Help
No.
No.
Recommended fields not provided:
Clinical validity,
Clinical utility,
Target population,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Comments:
Help
Sequence analysis of the entire coding region and intron/exon boundaries is offered as part of a Congenital Muscular Dystrophy panel
Availability:
Help
Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
Help
PCR-based sequencing detects 99% of the reported mutations in the POMGnT1 gene. The sensitivity of DNA sequencing is over 99% for the detection of nucleotide base changes, small deletions, insertions and indels in the region analyzed.
Proficiency testing (PT):
Is proficiency testing performed for this test?
Help
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
Help
SIFT, POLYPHEN2, Align GVGD, Mutation Taster, Splicing Programs
Laboratory's policy on reporting novel variations Help
They are reported as such
SIFT, POLYPHEN2, Align GVGD, Mutation Taster, Splicing Programs
Laboratory's policy on reporting novel variations Help
They are reported as such
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:
Help
Category:
Not Applicable
Additional Information
Reviews:
Clinical resources:
Consumer resources:
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.