LQT2 is KCNH2 and it encodes for alpha (HERG: human Ether-a-go-go Related Gene) subunit of the potassium channel conducting IKr current the rapid component of the delayed rectifier current. HERG forms homotetramers in the plasmalemma to make up functional potassium channels. LQT2 is the second most common LQTS mutation, contributing about 35%-40% of mutations. LQT2 has a higher penetrance than LQT1 and it is more severe, especially in females.

SCN5A is the LQT3 gene and it encodes for cardiac sodium channel conducting the sodium inward current (INa). LQT3 mutation results in gain of function of the channel and hence is the allele of Brugada syndrome in which there is loss of function of the same channel. The prevalence of LQT3 is about 10-15% of LQTS. It is a more malignant form of LQTS and has poor response to beta-blockers.

The LQT4 gene ANK2 encodes for an intracellular protein (Ankyrin B) that regulates the proper intracellular localization of plasmalemmal ion channels like calcium channel, sodium channel, sodium/calcium exchanger and sarcoplasmic reticulum channels. Just as Brugada syndrome mutation is the allele of LQT3, LQT4 is mutation is the allele of catecholaminergic polymorphic ventricular tachycardia (CPVT).

KCNE1 is the LQT5 gene which encodes for beta (MinK) subunit of potassium channel conducting IKs. KvLQT1 (LQT1 gene) proteins form homotetramers and co-assemble with minK (KQT5 gene) subunits to form a functional potassium channel. Jervell and Lange-Nielsen syndrome due to homozygous KCNE1 mutation is called JLN2.

KCNE2 the LQT6 gene encodes the beta (MiRP) subunit of the potassium channel conducting the IKr current the rapid component of the delayed rectifier current. This variant is quite rate (less than 1%), has incomplete penetrance and very mild manifestations.

KCNJ2, the LQT7 gene mutation causes Andersen syndrome, characterised by long QT interval and dysmorphic facial appearance. KCNJ2 encodes Kir2.1, an inwardly rectifier potassium channel, which conducts the IK1 current. Due to the facial dsymorphism seen in Andersen syndrome, Kir2.1 is thought to play a major role in developmental signaling.

CACNA1c, the LQT8 gene mutation causes Timothy syndrome. The mutation causes nearly complete loss of voltage-dependent inactivation of calcium channels. The resultant prolonged calcium current delays repolarization and increases the risk of arrhythmia.

CAV3, the LQT9 gene mutation causes a rare form of LQTS. CAV3 encodes for caveolin 3 and has been linked with sudden infant death syndrome (SIDS).

Sodium channel B4 subunit (SCNB4) mutation has been linked with LQT10, a rare form of long QT syndrome in 2007.