Invitae Long QT Syndrome Panel


Test description

This test is for individuals with a clinical diagnosis of long QT syndrome (LQTS). The primary panel includes 13 genes that are definitively associated with LQTS or other inherited arrhythmia disorders that may present with clinical features similar to LQTS.

Individuals with clinical symptoms of LQTS may benefit from diagnostic genetic testing to establish or confirm diagnosis, clarify risks, or inform management. Asymptomatic members of a family with a known LQTS pathogenic variant may also benefit by avoiding activities and medications that can trigger symptoms.

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Primary panel (13 genes)


Add-on preliminary-evidence genes (4 genes)

Preliminary-evidence genes currently have early evidence of a clinical association with the specific disease covered by this test. Some clinicians may wish to include genes which do not currently have a definitive clinical association, but which may prove to be clinically significant in the future. These genes can be added at no additional charge. Visit our Preliminary-evidence genes page to learn more.


Alternative tests to consider

Long QT syndrome can also be ordered as part of broader panels to test for arrhythmia disorders. Depending on the individual’s family history, one of these broader panels may be appropriate. Any of these broader panels can be ordered at no additional charge.

Long QT syndrome (LQTS), Jervell and Lange-Nielsen syndrome (JLNS), Andersen-Tawil syndrome, Timothy syndrome

LQTS is a hereditary cardiac arrhythmia that can cause fainting, seizure-like episodes, and cardiac arrest in both children and adults. LQTS is caused by abnormal electrical conduction in the heart that results in a “corrected” prolonged QT interval (a measure of the time it takes for an electrical signal to travel through the heart). The QTc abnormality is often—but not always—visible on an electrocardiogram.

The symptoms of LQTS manifest most often during intense exercise or times of emotional stress, but they can also occur during auditory stimulation, dehydration/electrolyte imbalance, the post-partum period, or while the patient is at rest. LQTS may be the underlying cause of some cases of sudden infant death syndrome (SIDS).

One autosomal recessive subtype of LQTS, Jervell and Lange-Nielsen syndrome (JLNS), is characterized by congenital bilateral sensorineural hearing loss as well as early-onset (childhood) cardiac arrhythmias and a very prolonged QTc interval.

This test covers all the common genetic causes of LQTS. Pathogenic variants in three main genes account for a significant majority of LQTS cases (see the table below). The remaining genes on this panel rarely cause LQTS (ANK2, CACNA1C, CALM1, CALM2, CALM3, CAV3, KCNE1, KCNE2, KCNJ2, TRDN) or cause an unknown percentage of cases (AKAP9, KCNJ5, SCN4B, SNTA1).

Clinical sensitivity by gene
KCNQ1 ~40%
KCNH2 ~35%
SCN5A ~5%

Studies show that up to 5% of mutation-negative LQTS individuals will have a large deletion or duplication in one of the above genes. Deletion/duplication analysis is included in this test.
Clinical sensitivity for LQTS subtypes:

  • Jervell and Lange-Nielsen syndrome—KCNQ1 accounts for approximately 90% of cases. KCNE1 accounts for approximately 4% of cases.
  • Andersen-Tawil syndrome—KCNJ2 is the only gene that is currently known to be associated with this disorder.
  • Timothy syndrome—CACNA1C is the only gene that is currently known to be associated with this disorder.

Long QT syndrome is an autosomal dominant disorder, with the exception of the subtypes Jervell and Lange-Nielsen syndrome (JLNS) and TRDN-related LQTS, which are autosomal recessive.

LQTS exhibits reduced penetrance, meaning that not everyone who inherits a predisposition to develop it will go on to manifest symptoms. LQTS has variable age of onset and can present from infancy to adulthood.

Among Caucasians, the prevalence of LQTS has been estimated at 1 of every 2,000 apparently healthy live births. LQTS has been identified all over the world and in all ethnic groups.

This test may be considered for individuals with:

  • arrhythmia consistent with a diagnosis of LQTS
  • unexplained cardiac arrest

  1. Ackerman MJ, et al. HRS/EHRA expert consensus statement on the state of genetic testing for the channelopathies and cardiomyopathies this document was developed as a partnership between the Heart Rhythm Society (HRS) and the European Heart Rhythm Association (EHRA). 2011 Heart Rhythm Aug; 8(8):1308-1339. PMID: 21787999
  2. Itoh, H., et al. Long QT syndrome with compound mutations is associated with a more severe phenotype: a Japanese multicenter study. Heart Rhythm. 2010 Oct; 7(10):1411-8. PMID: 20541041
  3. Modell, S., et al. Genetic testing for long QT syndrome and the category of cardiac ion channelopathies. PLoS Currents. 2012 May; 3:e4f9995f69e6c7. PMID: 22872816
  4. NCBI GeneReviews. Long QT Syndrome. PMID: 20301308
  5. National Heart, Lung and Blood Institute. What is Long QT Syndrome?
  6. National Library of Medicine. Genetics Home Reference: Long QT syndrome
  7. National Library of Medicine. Genetics Home Reference: Romano-Ward Syndrome
  8. Priori, SG, et al. Executive summary: HRS/EHRA/APHRS expert consensus statement on the diagnosis and management of individuals with inherited primary arrhythmia syndromes. 2013. Heart Rhythm, Dec;10(12):e85-108. PMID: 23916535
  9. Schwartz PJ, et al. Impact of genetics on the clinical management of channelopathies. 2013 J Am Coll Cardiol. Jul 16:62(3):169-180. PMID: 23684683
  10. Tranebjærg, L, et al. Jervell and Lange-Nielsen Syndrome. 2002 Jul 29. In: Pagon, RA, et al, editors. GeneReviews (Internet). University of Washington, Seattle; Available from: PMID: 20301579

For links to published management guidelines for cardiology conditions, please refer to our Management guidelines page.

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, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Assay notes

Please note, variants common in the general population that have been reported as modifiers of the QT interval are not included in the primary report, but are available in an unreported variant supplement by request.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
AKAP9 NM_005751.4
ANK2 NM_001148.4
CACNA1C NM_000719.6
CALM1 NM_006888.4
CALM2 NM_001743.4
CALM3 NM_005184.2
CAV3 NM_033337.2
KCNE1 NM_000219.5
KCNE2 NM_172201.1
KCNH2 NM_000238.3, NM_172057.2
KCNJ2 NM_000891.2
KCNJ5 NM_000890.3
KCNQ1 NM_000218.2
SCN4B NM_174934.3
SCN5A NM_198056.2
SNTA1 NM_003098.2
TRDN NM_006073.3