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Condition report · Cardiovascular

Long QT Syndrome

Whole genome sequencing identifies the specific ion channel mutations causing Long QT Syndrome, enabling genotype-guided therapy and cascade screening for asymptomatic relatives.

A condition report looks for rare variants known to cause the conditions it covers.

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About this condition

A heart rhythm condition in which the heart muscle takes longer than normal to recharge between beats, seen as a prolonged QT interval on an ECG. It can cause fainting, seizures or sudden cardiac arrest, often triggered by exercise, emotion or certain medicines.

Long QT Syndrome (LQTS) is a cardiac channelopathy characterized by delayed ventricular repolarization, visible on ECG as a prolonged QTc interval (>470ms in males, >480ms in females). This electrical abnormality creates a substrate for torsades de pointes, a life-threatening arrhythmia that can cause syncope and sudden cardiac death. LQTS affects approximately 1 in 2,000 to 2,500 people and accounts for an estimated 3-10% of sudden cardiac death in children and young adults. There are at least 17 genetic subtypes, but three account for approximately 75% of cases: LQT1 (KCNQ1, ~35%), LQT2 (KCNH2, ~30%), and LQT3 (SCN5A, ~10%). Inheritance is predominantly autosomal dominant; the rare autosomal recessive form (Jervell and Lange-Nielsen syndrome) combines LQTS with congenital sensorineural deafness.

The three major genes encode cardiac ion channels with distinct functions. KCNQ1 and KCNH2 encode potassium channels (IKs and IKr) that repolarize the ventricle; pathogenic variants reduce potassium current, delaying repolarization. SCN5A encodes the cardiac sodium channel; mutations in LQTS cause gain-of-function variants that permit persistent inward sodium current during repolarization, also prolonging the QT interval. The genotype-phenotype correlation is clinically important: LQT1 and LQT2 arrhythmias are typically triggered by physical exertion or emotional stress; LQT3 arrhythmias often occur at rest or during sleep. Approximately 25% of clinically diagnosed LQTS patients receive no molecular diagnosis from standard genetic testing.

Identifying a pathogenic LQTS variant transforms management from symptomatic treatment to family-based prevention. Genetic confirmation enables cascade testing of relatives, identifying asymptomatic mutation carriers who may have normal resting ECGs (up to 36% of KCNQ1 carriers show normal QTc). Beta-blockers are first-line therapy and have been shown to reduce sudden death risk by approximately 60%; implantable cardioverter-defibrillators (ICDs) are indicated for those who remain symptomatic despite medications. Gene-specific triggers inform lifestyle counseling: LQT1 carriers avoid strenuous exercise; LQT2 carriers avoid acoustic triggers; LQT3 carriers receive bedtime monitoring. Genetic information also enables reproductive counseling and prenatal testing options.

LQT1, LQT2, and LQT3 have distinct mechanistic bases (potassium channel loss vs. sodium channel gain), genotype-specific triggers (exercise/stress vs. sleep/rest), and different responses to beta-blockade; genotyping fundamentally alters management strategy.

The condition we analyse

A disorder of cardiac repolarisation marked by a prolonged QT interval and a risk of dangerous ventricular arrhythmias such as torsades de pointes.

What a diagnosis changes

Beta-blockers, ICD placement, activity restriction, genetic counseling

Genes analysed

Also known as

ventricular arrhythmia associated with long QT syndrome

Includes 26 related subtypes ↓
  • Andersen-Tawil syndrome
  • cardiac arrhythmia, ankyrin-B-related
  • familial long QT syndrome
  • Jervell and Lange-Nielsen syndrome
  • Jervell and Lange-Nielsen syndrome 1
  • Jervell and Lange-Nielsen syndrome 2
  • long QT syndrome 1
  • long QT syndrome 10
  • long QT syndrome 11
  • long QT syndrome 12
  • long QT syndrome 13
  • long QT syndrome 14
  • long QT syndrome 15
  • long QT syndrome 16
  • long QT syndrome 2
  • long QT syndrome 3
  • long QT syndrome 4
  • long QT syndrome 5
  • long QT syndrome 6
  • long QT syndrome 8
  • long QT syndrome 9
  • Timothy syndrome
  • Timothy syndrome type 1
  • Timothy syndrome type 2
  • Timothy syndrome, atypical type
  • Timothy syndrome, classic type
MONDO:0002442MedGen 44193

Why whole genome sequencing

Standard LQTS panels cover the major genes but leave 25% of patients genetically undiagnosed. They also cannot detect all structural variants.

One-quarter of clinically diagnosed LQTS patients have negative panels

Targeted LQTS panels typically cover KCNQ1, KCNH2, SCN5A, and 10-14 additional genes. Yet approximately 25% of patients who meet clinical criteria for LQTS receive no molecular diagnosis. Exon-level or whole-gene deletions/duplications in KCNH2 or KCNQ1, found in approximately 3% of LQTS patients, may not be detected depending on sequencing methodology. Additionally, panels test only known LQTS-associated genes; the "missing heritability" may involve variants in novel genes, non-coding regulatory variants affecting ion channel expression, or structural variants that standard panels cannot interrogate. Up to 36% of KCNQ1-related LQTS carriers have normal resting QTc, meaning ECG screening alone also misses carriers.

A finding enables genotype-specific prevention and family screening

When a pathogenic LQTS variant is identified, clinical management becomes genotype-informed. Beta-blockers (which reduce sudden death risk by ~60%) are initiated even in asymptomatic relatives. Gene-specific counseling applies: LQT1 carriers avoid strenuous exercise (highest arrhythmia risk during exertion), LQT2 carriers avoid auditory triggers (loud noises can provoke syncope), LQT3 carriers optimize nighttime monitoring. ICD placement is informed by genotype and family history. Cascade testing identifies asymptomatic relatives, often discovered because they have normal QTc intervals on ECG, enabling preventive therapy before symptoms occur. For young athletes in families with LQTS, genetic testing and pre-participation ECG screening are life-saving interventions.

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