Clinical utility gene card for: Long-QT syndrome

1.1 Name of the disease Long-QT syndrome (LQT, LQTS, Romano-Ward syndrome, subgroups: Jervell & Lange-Nielsen syndrome, Andersen-Tawil syndrome, Timothy syndrome, Ankyrin-B syndrome, Cardiac-only Timothy syndrome, Triadin knockout syndrome). Comment: It may be appropriate to limit the use of numbered LQTS to LQTS 1–3 and the remaining to their pathogenic basis, such as CALM -LQTS rather than LQT14 [ 1 ]. 1.2 OMIM# of the disease #192500 (LQT1, KCNQ1-LQTS) #613688 (LQT2, KCNH2-LQTS) #603830 (LQT3, SCN5A-LQTS) #600919 (LQT4, ANK2-LQTS) #613695 (LQT5, KCNE1-LQTS) #613693 (LQT6, KCNE2-LQTS) #170390 (LQT7), (KCNJ2-)Andersen-Tawil syndrome #601005, 618447 (LQT8), (CACNA1C-)Timothy syndrome #611818 (LQT9, CAV3-LQTS) #611819 (LQT10, SCN4B-LQTS) #611820 (LQT11, AKAP9-LQTS) #612955 (LQT12, SNTA1-LQTS) #613485 (LQT13, KCNJ5-LQTS) #616247 (LQT14, CALM1-LQTS) #616249 (LQT15, CALM2-LQTS) #114183 (LQT16, CALM3-LQTS) n.a. (LQT 17, TRDN-LQTS) #220400 JERVELL AND LANGE-NIELSEN SYNDROME 1; JLNS1 #612347 JERVELL AND LANGE-NIELSEN SYNDROME 2; JLNS2 Legend to Table 1.2.: Table 1.2 reflects the previous entries in OMIM. As for several of the entries, there is only disputed evidence for disease causation, those entries that are now regarded as having disputed evidence were presented in italics. 1.3 Name of the analysed genes or DNA/chromosome segments and OMIM# of the gene(s) LQT1: KCNQ1, 11p15.5-p.15.4; 607542 LQT2: KCNH2, 7qq36.1; 152427 LQT3: SCN5A, 3p22.2; 600163 LQT4: ANK2, 4q25-q26; 106410 LQT5: KCNE1, 21q22.12; 176261 LQT6: KCNE2, 21q22.11; 603796 LQT7:KCNJ2, 17qq2432; 600681 LQT8: CACNA1C, 12p13.33; 114205 LQT9: CAV3, 3p25.3; 601253 LQT10: SCN4B, 11q23.3; 608256 LQT11:AKAP9, 7q21.2; 604001 LQT12: SNTA1, 20q11.21; 601017 LQT13: KCNJ5, 11q24.3; 600734 LQT14: CALM1, 14q32.11; 114180 LQT15: CALM2, 2p21; 114182 LQT16: CALM3, 19q13.32; 114183 TRDN-LQTS: 6q22.31; 603283 ATS: KCNJ2, 17qq2432; 600681 JLNS1: KCNQ1, homozygous or compound heterozygous, 11p15.5-11p15.4; 607542 JLNS2: KCNE1, homozygous or compound heterozygous, 21q22.12; 176261 TS: CACNA1C, 12p13.33; 114205 1.3.1 Core genes (irrespective if being tested by Sanger sequencing or next-generation sequencing) (Table 1 ) Table 1 Core genes [ 1 ]. Full size table 1.3.2 Additional genes with disease gene validity (if tested by next-generation sequencing, including whole exome/genome sequencing and panel sequencing) (Table 2 ) Table 2 Reported genes with disease validity for LQTS [ 1 ]. Full size table 1.4 Mutational spectrum Table 3 Classification of genetic evidence for genes reported to be associated with LQTS based on the work of a multicentered, international clinical domain channelopathy working group [ 1 , 4 ]. Full size table Out of the 17 genes reported to be associated with LQTS, 3 genes ( KCNQ1, KCNH2, SCN5A ) are classified having definitive evidence as a genetic cause for LQTS. In more than 90% of the positive LQTS cases a variant affecting function is found in these three core genes. In addition, CALM1, CALM2, CALM3 and TRDN have a definitive or strong evidence for disease causation, but are associated with specific features. For variants affecting function in the three CALM genes, LQTS may present during infancy or early childhood with heart block and severe QT prolongation. At least 30% of patients with clinical clear LQTS are genotype elusive. Common variations likely contribute to phenotype in cases without a known Mendelian variant, but it is likely that there are other genetic and non-genetic factors involved [ 2 ]. Cases with TRDN mutations presented during early childhood with QT prolongation, negative T waves in precordial leads and exercise-induced arrhythmia related to homozygous or compound heterozygous disease-associated variants. Cases with biallelic loss-of-function variants in TRDN can present with either a CPVT or LQTS-like phenotype. Prolonged QTc is not always observed. In cases where it is, it can be classified as atypical LQTS but this is not always the case. The gene CACNA1C was reported to have a moderate evidence for disease causation in the absence of multiorgan involvement as in Timothy syndrome. The level of evidence for the gene KCNJ2 was only limited for the cardio-specific phenotype of LQTS, whereas both genes ( CACNA1C and KCNJ2 ) were classified to have definitive evidence for causing multiorgan syndromes (respectively: Timothy syndrome and Andersen-Tawil syndrome). Timothy syndrome might be associated with distinctive facial features, developmental delay, endocrine abnormalities and congenital heart defects besides bradycardia, QT prolongation and polymorphic arrhythmias [ 3 ]. Extracardiac manifestations of Andersen-Tawil syndrome may present as hypo-or hypercalemic episodes of paralysis (periodic paralysis) and morphological characteristics as low set ears, clinodactyly or hypertelorism. Andersen-Tawil syndrome is still classified as LQTS although prominent U waves tempted to determine a prolonged QT interval due to inclusion of the U wave [ 4 ]. Variants affecting function in the genes AKAP9, ANK2, CAV3, KCNE2, KCNJ5, SCN4B and SNTA1 are classified as having disputed evidence of disease validity and were, therefore, not included in Tables 1 – 3 [ 1 , 4 ]. The spectrum of disease-associated variants (of the loss-of-function subtypes) contains practically all types of variants affecting function (missense, nonsense, splice site, deletions and insertions). Most patients are heterozygous for a variant affecting function, but in ~5% of the cases, patients carry two disease-associated variants in the same or different genes. 1.5 Analytical validation Sequencing of all coding exons and intron-exon boundaries of the eligible genes as listed above. Analysis can be performed by Sanger sequencing, (as part of a (cardio) defined gene panel) targeted next-generation sequencing or by whole exome/genome sequencing. Deletions/duplications can be identified using different methods. For instance, multiplex ligation-dependent probe amplification, quantitative PCR, etc. Sequencing by the Sanger method is predicted to detect >99% of variants in the target regions. Sequencing of both strands (forward and reverse) is recommended. An independent analysis of a second sample of the patient is warranted. Using NGS as the sequencing method, the sensitivity will depend on the characteristics of test, including (sequencing strategy (e.g. panel/exome/genome), enrichment method), coverage of target regions, base quality and read depth. Classification of detected variants should be performed according to published standards (e.g. standards of the American College of Medical Genetics and Genomics (ACMG) [ 5 ] and should be used with customisation for the specific features of LQTS and its associated genes. 1.6 Estimated frequency of the disease (Incidence at birth (‘birth prevalence’) or population prevalence. If known to be variable between ethnic groups, please report): 1:2,000 in the general population. It may be assumed that the prevalence is of comparable magnitude in different populations [ 6 ]. 1.7 Diagnostic setting Yes. No. A. (Differential) diagnostics ⊠ ☐ B. Predictive Testing ☐ ⊠ C. Risk assessment in Relatives ⊠ ☐ D. Prenatal ⊠ ☐ Comments: Comment 1: Prenatal diagnosis of Long-QT syndrome is indicated in very exceptional situations only and is asked for extremely rarely. Comment 2: Among clinically definite LQTS cases the three most frequently affected genes with a disease-causing change are KCNQ1, KCNH2 and SCN5A . Most of the LQTS patients are heterozygous for a variant affecting function, but in ~5% of the cases, patients carry two variants affecting function in the same gene (compound heterozygous or homozygous), or in different genes (digenic) [ 7 , 8 ]. In general, this is associated with a more severe phenotype with younger age of onset and more adverse events, suggesting a gene-dosage effect. Comment 3: Copy number variation might be present in 3–12% of patients in core genes [ 9 , 10 , 11 , 12 , 13 ]. 2. Test characteristics genotype or disease A: true positives C: false negative present absent B: false positives D: true negative Test pos. A B sensitivity: specificity: A/(A+C) D/(D+B) neg. C D pos. predict. value: neg. predict. value: A/(A+B) D/(C+D) 2.1 Analytical sensitivity (proportion of positive tests if the genotype is present in the analyte) 2.1.1 if tested by conventional Sanger sequencing Close to 100% if complete Sanger sequencing and deletion/duplication (MLPA) analysis of the affected clinically important regions of each gene is performed. MLPA is indicated for KCNQ1 , KCNH2 and KCNJ2 . In SCN5A there is insufficient evidence for CNV causing a gain-of-function. But this nearly 100% analytical sensitivity includes variants affecting function as well as variants that are just innocent bystanders where the clinical impact has to be proven subsequently. Potential non-coding pathogenic variants in the 3 core genes may remain undetected by standard sequencing approaches, e.g. deep intronic splice variants. 2.1.2 if tested by Next-generation sequencing Analytical sensitivity for single nucleotide variants, insertions and deletions: >99% at ≥50× read depth if MLPA and bioinformatic copy number variation (CNV) analysis is included (targeted next-generation sequencing panel approach) [ 14 ]. Lack of coverage of specific target regions is a common problem of all NGS platforms. In some cases, the problem can be particularly relevant. For example, some exons of KCNH2 are frequently not completely covered due to their high CG-rich sequence. Thus, additional analysis by Sanger sequencing of these uncovered regions is often required [ 15 , 16 ]. Core genes ( KCNQ1 , KCNH2 , SCN5A ) including flanking splice sites should be entirely and sufficiently covered (at least 20x). Potential non-coding pathogenic variants in the 3 main genes may remain undetected by standard sequencing approaches, e.g. deep intronic splice variants. 2.2 Analytical specificity (proportion of negative tests if the genotype is not present) 2.2.1 if tested by conventional Sanger sequencing Close to 100% if complete sequencing and MLPA of the affected gene is performed. But not finding a disease-associated variant rejects by no means the diagnosis LQTS in definite clinical cases as in about 30% the underlying cause or causative genes are still not known. 2.2.2 if tested by Next-generation sequencing See 2.2.1 2.3 Clinical sensitivity (proportion of positive tests if the disease is present) The clinical sensitivity can be dependent on variable factors such as age or family history. In such cases, a general statement should be given, even if a quantification can only be made case by case. 2.3.1 if tested by conventional Sanger sequencing On average the detection rate of variants affecting function for the most frequent LQTS disease genes ( KCNQ1 , KCNH2 , and SCN5A ) is about 60–70% [ 17 ]. 2.3.2 if tested by next-generation sequencing Extra sensitivity due to sequencing additional genes by NGS is minimally higher as each additionally tested gene mentioned in table a.1.3.1 and 1.4 increases sensitivity slightly. 2.4 Clinical specificity (proportion of negative tests if the disease is not present) The clinical specificity can be dependent on variable factors such as age or family history. For instance, some patients show an incomplete phenotype, in some individuals the diagnosis is established in adulthood, because of a late onset of symptoms. These cases can likely result in a lower sensitivity. In such cases, a general statement should be given, even if a quantification can only be made case by case. 2.4.1 if tested by conventional Sanger sequencing About 95%, however, the rate of rare variants of uncertain significance (i.e. non-synonymous genetic variation) in Caucasians is about 4–8% in Non-Caucasian in the LQTS 1–3 genes [ 18 ]. 2.4.2 If tested by next-generation sequencing See 2.4.1 2.5 Positive clinical predictive value (life time risk to develop the disease if the test is positive) Before the age of 40 years roughly 40% of (untreated) patients with LQTS1 and LQTS2 become symptomatic. In LQTS3 this is less, but symptoms may be more severe. Phenotypic expression of the disorder is time-dependent and LQTS subjects maintain a high risk for life-threatening cardiac events after age 40 years, which seems to be less high for LQTS1 [ 19 , 20 ]. 2.6 Negative clinical predictive value (Probability not to develop the disease if the test is negative) (Probability not to develop the disease if the test is negative). Assume an increased risk based on family history for a non-affected person. Allelic and locus heterogeneity may need to be considered. Index case in that family had been tested: If the index case in that family had been tested and a non-equivocal disease-associated variant had been found in the index patient and the non-affected proband is not a carrier of the identified disease- associated variant close to 100%. In those cases the risk remains as small as the prevalence of the disease in the general population. Index case in that family had not been tested: If the patient is clinically affected (prolonged QTc with or without syncope) the index patient has a chance of about 60–70% carrying a variant affecting function. But only in very rare cases there is an indication for performing LQTS genetic testing in a clinically unaffected relative when the index case has not been tested. This could be imaginable when in an index case there is a strong clinical suspicion of LQTS and there is no DNA available or the index patient refuses genetic testing. Usually, there is no indication for genetic testing in a clinically unaffected family member with unclear genetic status of the index patient if the ECG is normal.