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PAX6 mutation analysis
Clinical Genetic Test
Help
offered by
Amsterdam UMC Genome Diagnostics
View lab's test page
LinkOut
GTR Test Accession: Help GTR000500345.7
INHERITED DISEASEDYSMORPHOLOGYOPHTHALMOLOGY ... View more
Last updated in GTR: 2018-11-15
View version history
Last annual review date for the lab: 2024-04-16 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; ...
Conditions (2): Help
Aniridia 1; Anophthalmia-microphthalmia syndrome
Genes (1): Help
PAX6 (11p13)
Methods (2): Help
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
For patients suspected to this particular and patients with a …
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
Amsterdam UMC Genome Diagnostics
View lab's website
View lab's test page
Test short name: Help
PAX6
Specimen Source: Help
  • Amniocytes
  • Amniotic fluid
  • Buccal swab
  • Cell culture
  • Chorionic villi
  • Cord blood
  • Fetal blood
  • Fibroblasts
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Peripheral (whole) blood
  • Saliva
  • View specimen requirements
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • 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
Using our website
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Test additional service: Help
Custom Prenatal 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
No
Test strategy: Help
Simultaneous bi-directional sequencing of all coding exons and MLPA
Pre-test genetic counseling required: Help
Yes
Post-test genetic counseling required: Help
Yes
Recommended fields not provided:
Test Order Code, Lab contact for this test
Conditions Help
Total conditions: 2
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
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; Prognostic; Risk Assessment; Screening
Target population: Help
For patients suspected to this particular and patients with a positive family history for this disease, gene sequence analysis is recommended as the first step in mutation identification.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
The 5-classes classification method (Alamut)

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
Clinical validity, Clinical utility, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Procedure: Help
DNA is extracted from the patient specimen, PCR amplification and sequence analysis of the entire coding region/ or indicated exons plus additional flanking intronic or other non-coding sequence. Sanger sequencing is carried out and the sequence is visualized on a capillary sequencer. Sequencing is performed separately in both the forward … View more
Test Confirmation: Help
Confirmation of identified mutations is done in an independent experiment.
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
This test detects >99% of described mutations
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
European Molecular Genetics Quality Network, EMQN

Description of PT method: Help
For Proficiency Testing, both external and internal, we have Sanger-sequenced extensive numbers of PCR fragments, and the error rate is less than 0.01% (99.99% accuracy). We also have performed MLPA of large numbers of samples with the maximal possible technical accuracy (>99.8%). Technical specificity for methods used in our laboratory … View more
VUS:
Software used to interpret novel variations Help
Alamut (Interactive Biosoftware), including AGVGD, PolyPhen-2, SIFT and MutationTaster for missense predictions and MAXEntScan, NNSPLICE, GeneSplicer and Human Splicing Finder for splice predictions

Laboratory's policy on reporting novel variations Help
Our laboratory reports class 3 (unknown pathogenicity), class 4 (likely pathogenic) and class 5 (certainly pathogenic) variants.
Recommended fields not provided:
Assay limitations, Description of internal test validation method, Citations for Analytical validity, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: Not Applicable
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.