KCNE1 and KCNE2 variants in Patients with Long QT Syndrome

Most cardiovascular diseases have a genetic background. Many of these diseases have a Mendelian  (single gene disorders)  inherited pattern. For instance, among the arrhythmias, long QT syndrome could be named. This syndrome is a fatal ventricular arrhythmia characterized by an increase in QT interval on the electrocardiogram. An increase in QT may lead to torsade de points and premature heart death. Long QT syndrome has two dominant autosomal inherited patterns  (commonly Romano-Ward syndrome)  and an autosomal recessive form with congenital deafness  (less commonly Jerrvel-Lange-Nielsen syndrome which is characterized by congenital deafness, prolongation of the QT interval, syncopal attacks due to ventricular arrhythmias, and a high risk of sudden death). The prevalence of this disease is one person per 2000 and it usually affects children and adolescents in the age group of 14 years.In addition to the congenital form that occurs due to variants in genes encoding sodium, potassium, and calcium ion channels, the consumption of certain drugs or electrolyte disturbances can also increase the QT intervals. About 20 genes are known to cause long QT syndrome the KCNQ1 gene causing LQTS1; KCNH2 causing LQT2; SCN5A causing LQT3; ANK2 causing LQTS4; KCNE1 causing LQTS5; KCNE2 causing LQT6; KCNJ2 causing LQTS7; CACNA1c causing LQTS8; CAV3 causing LQTS9; SCN4B causing LQTS10; AKAB9 causing LQTS11; SNTA1 causing LQTS12; KCNJ5 causing LQTS13; CALM1 causing LQTS14; CALM2 causing LQTS15; CALM2 causing LQTS16; and TRDN causing atypical type of LQTS (LQTS17), among which variants in the KCNE1  and KCNE2 genes encoding Potassium voltage-gated channel subfamily E member 1 and 2 account for less than 2 % of the genotype. KCNE1 and 2 proteins act as ancillary proteins assembling as a beta subunit of a voltage-gated potassium channel complex of pore-forming alpha subunits. Jerrvel-Lange-Nielsen syndrome is due to KCNQ1 (JLNS1) KCNE1 (JLNS2). Here, KCNE1 and KCNE2 variants are studied among Iranian affected families.

 Genomic DNA was extracted from peripheral whole blood by salting out method. A pair of primers was designed for each gene and checked using the Primer blast and Nucleotide blast sites. The coding regions of each gene were amplified by polymerase chain reaction (PCR). Sanger sequencing was applied to find out the variants.

 In this study, a total of 50 patients (ages from 7 months to 25 years) with QTc between 338 ms to > 600 ms including 37 patients with Romano-Ward Syndrome  phenotype and 4 patients with Jerrvel-Lange-Nielsen Syndrome   phenotype were studied. The most common symptoms and signs were syncope (in 23 cases), premature heart death  (in 11 cases), palpitations  (in 11 patients), notched T-wave (in 6 cases), chest pain (in 5 cases)  of and epilepsy  (in 5 cases). p.Ser38Gly (c.112 A > G) in KCNE1  was seen in 18 homozygous cases and 22 heterozygous cases followed by the next variant  (c. * 132 A > G)  in the 3 ′ UTR region in 2 patients; a 19-month-old boy with Romano-Ward Syndrome  phenotype and a history of palpitations  (Schwartz Score3, QTC524ms)  and the other patient was a 3-year-old boy with a Jerrvel-Lange-Nielsen Syndrome   phenotype and a history of syncope with stress, deafness and notched T-wave  (Schwartz score 7.5, QTC > 600 ms). The variant  (c. * 124 A > G)  located in the 3 ′ UTR region was seen in 11 patients  (3 patients with Jerrvel-Lange-Nielsen Syndrome   phenotype). Given that variant  (c. * 132A> G)  KCNE1  is predicted by the HSF site to be in a region that is a potential enhancer, it may break Exonic Splicing Enhancers. c.29 C > T  (p.Thr10Met)  in heterozygous form was found in a 5-year-old Kurdish male with a history of cardiac pacemaker, cardiac arrest and stress syncope  (QTC > 500 ms, Schwartz Score 5) which was affected by congenitally lack of right kidney. Another heterozygous variant was observed in  (c.325 G > A) (p.Val109Ile)  in a 12-year-old boy with a history of ICD implantation and stress syncope (QTc > 480 ms, Schwartz Score 5). The patient's family history showed that one of the family members had proband-like symptoms and the other two had atherosclerosis.KCNE2 variants were also found in our patients; c.-12-44 C > T was found in 6 cases, 2 of which had Schwartz score zero and 2 others had Schwartz score 4, 5. In addition, one patient had JERRVEL-LANGE-NIELSEN SYNDROME   phenotype and 5 had Romano-Ward Syndrome  . Another intron variant  (c.-12-16 A > G) was detected in 2 cases, one patient with Schwartz score zero and the other one with Schwartz score five. The heterozygous exon variant was also found in 2 unrelated patients  (p.Thr8Ala, c.22 A > G), case number 15, a 3.5-year-old boy with a history of 2 fainting and sinus tachycardia and taking a quarter of captopril twice a day which undergone mitral valve repair. Case number 50 was also a 3.5-year-old boy from Tehran with a history of syncope, epilepsy and taking propranolol at a dose of 10 mg every 8 hours  (Schwartz score 5). 3 members of this recent family had a heart attack, one of whom died at the age of 16. Also, proband's father had epileptic seizures before puberty.A heterozygous variant, p.Ile57Thr  (c.170 T > C) was found in a 13-year-old boy with a history of chest pain, palpitations and anemia  (QTc 371 – 546 ms, Schwartz score 3).Briefly, fifty patients referring to Rajaei Cardiovascular Hospital who negative for common genes were selected. Coding regions of KCNE1  and KCNE2 genes were amplified and directly sequenced to find possible variants of these genes. Bioinformatic tools were used to predict pathogenicity of the variants. KCNE1  variants included c. * 132 A > G and c. * 124 A > G in 3’ UTR and c. 325 G > A and c. 112 A > G in exonic regions were found. In addition, two intronic variants, c. -12-16 A > G and c.-12-44 C > T and two exonic variants c.170 T > C and c.22 A > G were observed in KCNE2 gene. Bioinformatics analysis showed pathogenicity of the variants. The exon variant  (c. 112A > G ; p. Ser38Gly)  and 2 regulatory variants  (c. * 132 A > G)  and  (c. * 124 A > G) were benign and 2 exon variants  (c.29 C > T and c 325 G > A) showed conflicting interpretations of pathogenicity and uncertain significance, respectively. In the case of the KCNE2 gene, two exonic variants (c. 22 A > G) and  (c. 170 T > C)  are categorized as disease causing variants based on the predictions of SIFT, Polyphen2 and Mutation Taster.

 KCNE1  and KCNE2 variants have a high frequency among Iranian patients with Long QT syndrome. Therefore, study of pathogenicity of these two genes and other KCNE gene family is recommended to include in genetic tests for Iranian patients. Due to the fact that the Iran population is composed of different ethnicities and subpopulations and the frequency and type of causative mutations may be different . Therefore, it is suggested that it be studied separately in different subpopulations and ethnicities of Iran.