SCN5A mutation analysis - Clinical Genetic Test - GTR

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SCN5A mutation analysis

Clinical Genetic Test

offered by

Amsterdam UMC Genome Diagnostics

View lab's test page

GTR Test Accession: GTR000500447.5

INHERITED DISEASECARDIOVASCULARSYNDROMIC DISEASE ... View more

Last updated in GTR: 2018-11-15

Last annual review date for the lab: 2023-04-13 Past due

At a Glance

Test purpose:

Diagnosis; Mutation Confirmation; Pre-symptomatic; ...

Conditions (6):

Brugada syndrome 1; Atrial fibrillation, familial, 10; Dilated cardiomyopathy 1E; ...

Genes (1):

SCN5A (3p22.2)

Methods (1):

Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis

Target population:

Patients suspected to this particular and patients with a positive …

Clinical validity:

Not provided

Clinical utility:

Establish or confirm diagnosis; Predictive risk information for patient and/or family members

Ordering Information

Offered by:

Amsterdam UMC Genome Diagnostics
View lab's website
View lab's test page

Test short name:

SCN5A

Specimen Source:

Buccal swab
Cell culture
Cord blood
Fibroblasts
Frozen tissue
Isolated DNA
Peripheral (whole) blood
Saliva
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician
Physician Assistant

Contact Policy:

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:

Using our website
Order URL

Test service:

Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings

Test additional service:

Custom mutation-specific/Carrier testing

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Test strategy:

Simultaneous bi-directional sequencing of all coding exons

Pre-test genetic counseling required:

Yes

Post-test genetic counseling required:

Yes

Recommended fields not provided:

Test Order Code, Lab contact for this test

Conditions

Total conditions: 6

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 1

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 1

Method Category

Test method

Instrument

Sequence analysis of the entire coding region

Bi-directional Sanger Sequence Analysis

Applied Biosystems 3730 capillary sequencing instrument

Clinical Information

Test purpose:

Diagnosis; Mutation Confirmation; Pre-symptomatic; Predictive; Screening

Clinical utility:

Establish or confirm diagnosis
Predictive risk information for patient and/or family members

Target population:

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?
The 5-classes classification method (Alamut)

Will the lab re-contact the ordering physician if variant interpretation changes?
Yes.

Recommended fields not provided:

Clinical validity, 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:

Confirmation of identified mutations is done in an independent experiment.

Test Confirmation:

Confirmation of identified mutations is done in an independent experiment.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

This test detects >99% of described mutations

Assay limitations:

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 insertions, or mutations outside the analyzed regions will not be detected.

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
European Molecular Genetics Quality Network, EMQN

Description of PT method:
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
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
Our laboratory reports class 3 (unknown pathogenicity), class 4 (likely pathogenic) and class 5 (certainly pathogenic) variants.

Recommended fields not provided:

Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Category: Not Applicable

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View SCN5A variations in ClinVar

RefSeqGene

Coriell Institute for Medical Research

Consumer resources:

Genetic Alliance

MalaCards

MedlinePlusGenetics (GHR)

MedlinePlus

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.