CNGA3 mutation analysis
GTR Test Accession: Help GTR000518793.4
INHERITED DISEASEOPHTHALMOLOGYNERVOUS SYSTEM ... View more
Last updated in GTR: 2018-11-15
Last annual review date for the lab: 2024-04-16 LinkOut
At a Glance
Diagnosis; Mutation Confirmation; Pre-symptomatic; ...
Achromatopsia 2
Genes (1): Help
CNGA3 (2q11.2)
Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis
For patients suspected to this particular and patients with positive …
Not provided
Not provided
Ordering Information
Offered by: Help
Amsterdam UMC Genome Diagnostics
View lab's website
View lab's test page
Test short name: Help
CNGA3
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
Maternal cell contamination study (MCC)
Uniparental Disomy (UPD) Testing
Test additional service: Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
No
Test strategy: Help
Simultaneous bi-directional sequencing of all coding exons
Pre-test genetic counseling required: Help
Yes
Post-test genetic counseling required: Help
Yes
Recommended fields not provided:
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: 1
Method Category Help
Test method Help
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 positive familial 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)

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Carrier testing is performed with a reduced pricing rate and in selected cases at no cost after contact with the lab.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
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 visualised on a capillary sequencer. Sequencing is performed separately in both the forward … View more
Test Confirmation: Help
confirmation of identified mutations 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 number of PCR fragments, and the error rate is less than 0.01% (99.99% accuracy). Also We had performed MLPA large numbers of samples, and NGS (used for increasing number of genes and panels in cardiogenetics, metabolic diseases, ophthalmogenetics and … 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:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
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.