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SCN5A

Alias

CDCD2; CMD1E; CMPD2; HB1; HB2; HBBD; HH1; ICCD; IVF; LQT3; Nav1.5; PFHB1; SSS1; VF1

Associated disorders

The SCN5A gene is associated with autosomal dominant Brugada syndrome (BrS) (MedGen UID: 468523), long QT syndrome (LQTS), type 3 (MedGen UID: 349087), dilated cardiomyopathy (DCM) (MedGen UID: 331341) and atrial fibrillation (MedGen UID: 462814). Other SCN5A-related conditions have been reported (OMIM: 600163). For information about the location of a SCN5A variant, please visit www.invitae.com/SCN5A-topology.

Pathogenic SCN5A variants cause 15%-30% of cases of BrS and 5% of cases of LQTS. Pathogenic SCN5A variants are a rare cause of DCM and are associated with an unknown percentage of atrial fibrillation.

The SCN5A gene encodes the alpha unit of the sodium channel protein type 5. Sodium channels control the flow of sodium ions in cardiac muscle cells. The electrical activity of cardiac muscle is controlled by the movement of potassium, sodium and calcium ions across cardiac muscle cell membranes. Mutations in genes that disrupt the function of a sodium channel are a common cause of inherited cardiac arrhythmias.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
SCN5A NM_198056.2