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PHKA2 - NGS including CNV analysis
Clinical Genetic Test
Help
offered by
Centogene AG - the Rare Disease Company
View lab's test page
LinkOut
GTR Test Accession: Help GTR000598684.1
CAP
INHERITED DISEASEDIGESTIVE SYSTEMENDOCRINOLOGY ... View more
Registered in GTR: 2022-10-13
View version history
Last annual review date for the lab: 2022-11-01 Past due LinkOut
At a Glance
Test purpose: Help
Diagnosis
Conditions (1): Help
Glycogen storage disease IXa1
Genes (1): Help
PHKA2 (Xp22.13)
Methods (2): Help
Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Not provided
Clinical validity: Help
This panel should be performed in all individuals suspected of …
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
Centogene AG - the Rare Disease Company
View lab's website
View lab's test page
Specimen Source: Help
  • Amniotic fluid
  • Bone marrow
  • Buccal swab
  • Cell culture
  • Chorionic villi
  • Dried blood spot (DBS) card
  • Fetal blood
  • Fibroblasts
  • Isolated DNA
  • Peripheral (whole) blood
  • Product of conception (POC)
  • Saliva
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Dentist
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
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.
How to Order: Help
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Result interpretation
Test additional service: Help
Custom mutation-specific/Carrier testing
Informed consent required: Help
Yes
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, Lab contact for this test, Test strategy, Test development
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 *
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: Help
Diagnosis
Clinical validity: Help
This panel should be performed in all individuals suspected of having an overlapping clinical phenotype. Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the condition, identify at-risk … View more
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
The interpretation of a variation as a VUS is done according to the practice guidelines provided by the American College of Medical Genetics (ACMG; ACMG recommendations for standards for interpretation and reporting of sequence variations).

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
No. We are performing a majority of carrier testing with reduced pricing and in selected cases at no cost.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes. In case of identification of mutation that can be present in non-affected family members, or after identification of highly specific genetic change, or in additional special situations we could contact the ordering physician again.
Research:
Is research allowed on the sample after clinical testing is complete? Help
After clinical testing is completed, with the patient’s signed consent, Centogene utilizes and archives the sample according to all regulatory guidelines and standards.
Recommended fields not provided:
Clinical utility, Target population, Sample negative report, Sample positive report
Technical Information
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
CENTOGENE has established stringent quality criteria and validation processes for variants detected by NGS. Variants with low sequenci ng quality and/or unclear zyg osity are confirmed by orthogonal methods. Consequently, a specificity of > 99.9% for all reported variants is warranted. Mitochondrial variants are reported for heteroplasmy levels of 15% … View more
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
VUS:
Software used to interpret novel variations Help
ALAMUT, integrating other programs (Polyphen-2, Mutation Taster, Alignment, ExPASy, BLAST) .

Laboratory's policy on reporting novel variations Help
Centogene has a common practice to report all variants found in genetic testing, including novel and previously reported variants. A number of criteria are used to support a variant as being potentially disease-causing, including segregation with disease status in other affected family members, absence from a control population, and location … View more
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
Not provided
Additional Information

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.