KCNQ1 mutation analysis
GTR Test Accession: Help GTR000500450.5
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; ...
Long QT syndrome 1; Jervell and Lange-Nielsen syndrome 1; Short QT syndrome type 2
Genes (1): Help
KCNQ1 (11p15.5-15.4)
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Patients suspected to this particular and patients with a positive …
Not provided
Establish or confirm diagnosis; Predictive risk information for patient and/or family members
Ordering Information
Offered by: Help
Amsterdam UMC Genome Diagnostics
View lab's website
View lab's test page
Test short name: Help
Specimen Source: Help
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 mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Test strategy: Help
Simultaneous bi-directional sequencing of all coding exons and MLPA
Pre-test genetic counseling required: Help
Post-test genetic counseling required: Help
Recommended fields not provided:
Conditions Help
Total conditions: 3
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 1
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Total methods: 2
Method Category Help
Test method Help
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; Predictive; Screening
Clinical utility: Help
Establish or confirm diagnosis
Predictive risk information for patient and/or family members
Target population: Help
Patients suspected to this particular and patients with a positive family history for the disease.
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
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 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
Assay limitations: Help
All coding sequences, including the flanking intron sequences are analyzed using direct sequencing. With this method we can detect point mutations and small deletions or insertions. The presence of larger deletions or duplications are analyzed by MLPA. Mutations outside the analyzed regions will not be detected.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help

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
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: Not Applicable
Additional Information

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