ClinVar Genomic variation as it relates to human health

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant is present in HGMD in 8 papers, in affected and unaffected individuals, with some suggesting benign, others pathogenic and one calling it a Finnish founder mutation. It is classified in ClinVar with 1 star as Likely benign by Invitae, VUS by GeneDx and risk factor by Blueprint genomics. It is not present in ExAC but has a max MAF in gnomAD of 0.12% (10/8048 Finnish alleles and 33 european alleles). Note from April 2016: This variant has not undergone full assessment. The following are preliminary notes: conflicting reports. Also very difficult to do the full NVA because most papers we do not have access at. Possibly upgrade to VUS4? OB 12/28/15: VUS4 based on the full NVA. Heidi agrees that it is VUS4 and does not meet criteria for reporting.

This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PP3.

The KCNH2 c.526C>T p.(Arg176Trp) missense has been widely reported in association with long QT syndrome (LQTS) and described as a founder variant in the Finnish population. Across a selection of the available literature, the variant has been identified in a heterozygous state in at least 100 of approximately 3,000 patients with LQTS or prolonged QTc intervals, and a significant increase in QTc in carriers compared to non-carriers has been demonstrated (Swan et al. 1999; Laitinen et al. 2000; Ackerman et al. 2003; Tester et al. 2006; Fodstad et al. 2004; Fodstad et al. 2006; Marjamaa et al. 2009; Giudicessi et al. 2012; Lahtinen et al. 2013; Koponen et al. 2015). Notably, however, many individual carriers remain asymptomatic and have QTc intervals that do not meet diagnostic criteria for LQTS. The variant has also been proposed to act as a risk factor for cardiac events; Koponen et al. (2018) reported a hazard ratio of cardiac events at age 18-40 years, before initiation of beta-blocker therapy, of 5.87 (95% CI 2.89-11.9). The p.(Arg176Trp) variant has also been identified in a compound or double heterozygous state with a second pathogenic variant, suggesting it may exert a modifying effect. This variant is reported at a frequency of 0.001231 in the European (Finnish) population of the Genome Aggregation Database (version 2.1.). This frequency is higher than expected given the known prevalence, penetrance, and inheritance of LQTS. Functional studies of the p.(Arg176Trp) variant have provided conflicting results. When the variant was expressed independently in COS-7 cells, a reduction in current density and tail current to approximately 25% of wildtype and a slight acceleration of deactivation kinetics was observed (Fostad et al. 2006). However, when co-expressed with wildtype, the current reduction was no longer present, suggesting the absence of a dominant-negative effect. In cardiomyocytes derived from iPS cells from an asymptomatic carrier, the rapid delayed potassium channel density was significantly reduced, and at low beating rates, the repolarization time was significantly prolonged compared to that in control cells (Lahti et al. 2012). However, no positive control variants were included and the potential influence of additional variants in the carrier from whom the cells originated was not excluded. In addition, in zebrafish, both wildtype and R176W KCNH2 showed a similar ability to rescue the effect of morpholino-mediated gene knockdown, suggesting a benign effect of the variant (Jou et al. 2013). This variant affects a conserved residue but is not located in a mutational hotspot or functional domain. While missense variants are a known mechanism of disease for LQTS, benign missense variants have been reported, including in the region surrounding position 176. Based on the collective evidence, the c.526C>T p.(Arg176Trp) variant is classified as a variant of uncertain significance for long QT syndrome.

The p.R176W variant (also known as c.526C>T), located in coding exon 4 of the KCNH2 gene, results from a C to T substitution at nucleotide position 526. The arginine at codon 176 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration has been identified in subjects with long QT syndrome (LQTS) and has been reported as a possible Finnish founder mutation (Swan H, J. Amer. Coll. Cardiol. 1999;34(3):823-9; Laitinen P, Hum. Mutat. 2000; 15(6):580-1; Fodstad H, Ann. Med. 2004;36 Suppl 1:53-63; Marjamaa A, Ann. Med. 2009;41(3):234-40; Donner BC, Cardiol Young. 2012; 22(3):360-3). Several studies indicate that carriers of this variant have moderately prolonged QT intervals on average (Fodstad H, Ann. Med. 2006; 38(4):294-304; Marjamaa A et al. Ann. Med., 2009;41:234-40; Koponen M et al. BMC Med Genet, 2018 04;19:56). However, this alteration has also been identified in apparently healthy individuals (Ackerman MJ et al. Mayo Clin. Proc. 2003;78:1479-87; Fodstad H, Ann. Med. 2006; 38(4):294-304; Maltese PE et al. Int Heart J. 2017;58(1):81-87). Two functional studies suggest this alteration has an impact on protein function (Fodstad H, Ann. Med. 2006 ; 38(4):294-304; Lahti AL, Dis Model Mech 2012 Mar; 5(2):220-30). Other studies do not detect a significant impact on protein function (Männikkö R et al. Br J Pharmacol, 2010 Jan;159:102-14; Jou CJ et al. Circ. Res. 2013;112:826-30; Soh MS et al. Ann Clin Transl Neurol, 2021 07;8:1422-1432). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited and conflicting at this time, the clinical significance of this alteration remains unclear.

ACMG categories: PM2,PP3

Variant summary: KCNH2 c.526C>T (p.Arg176Trp) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00035 in 80198 control chromosomes. The observed variant frequency is approximately 2.83 fold of the estimated maximal expected allele frequency for a pathogenic variant in KCNH2 causing Long QT Syndrome phenotype (0.00012), strongly suggesting that the variant is benign. c.526C>T has been reported in the literature in individuals undergoing limited gene to multigene panel testing for Long QT Syndrome/Arrhythmia and continues to be reported as a VUS/risk variant that is enriched in patients referred for diagnostic LQTS gene testing but lacking a molecular diagnosis (panel-negative) (example, Kapa_2009, Koponen_2015, Laitinen_2000, Mank-Seymour_2006, Marjamaa_2009, Swan_1999, van Lint_2019, Vatta_2021, Kozek_2021). These report(s) do not provide unequivocal conclusions about a penetrant inherited association of the variant with Long QT Syndrome. Co-occurrences with other pathogenic variant(s) have been reported (KCNQ1 c.1766G>A, p.Gly589Asp; KCNQ1 IVS7-2A>G), providing supporting evidence for a benign role (example, Koponen_2015, Fodstad_2006). However, the possibility of this variant exerting an additional in vivo phenotypic effect when present simultaneously with an apparent LQTS-causing mutation has also been proposed (Fodstad_2006). At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant as indicated by normal repolarization in the kcnh2-knockdown embryonic zebrafish (example, Jou_2013). The following publications have been ascertained in the context of this evaluation (PMID: 14661677, 16754261, 23303164, 19841300, 26063740, 34309407, 10862094, 17161064, 19160088, 10483966, 33517668, 30847666). Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments (VUS, n=9, likely benign, n=2, risk factor, n=1). Based on the evidence outlined above, the variant in isolation was classified as likely benign.

Criteria: BS1, PP2, PP3

Risk factor for disease development: PS4; PP1_strong; PS3_mod; PP2; PP3; BS1; BS2

Reported in association with LQTS but also present in asymptomatic individuals, control individuals, and individuals who harbor additional cardiogenetic variants referred for genetic testing at GeneDx or in published literature (PMID: 10483966, 10862094, 14661677, 17161064, 16754261, 22067087, 23098067, 24606995, 26063740, 28003625); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Electrophysiological studies suggest the presence of the p.(R176W) variant may lead to changes in HERG channel function under various experimental conditions; however, other functional studies suggest that this variant has a benign effect (PMID: 22052944, 16754261, 23303164, 34002542); This variant is associated with the following publications: (PMID: 14661677, 22067087, 25351510, 25467552, 32383558, 22429796, 17161064, 19160088, 24606995, 16754261, 16818214, 17222736, 23098067, 23651034, 22677073, 26063740, 27026928, 28003625, 27650965, 22949429, 28255936, 15176425, 29622001, 15541256, 19673885, 10862094, 19841300, 19862833, 21244686, 20875080, 21956039, 23193492, 22402074, 22659597, 23631430, 25554238, 26749013, 27064559, 30847666, 34002542, 23303164, 28988457, 32048431, 31539150, 31737537, 33517668, 33435129, 34426522, 32659924, 22052944, 10483966, 35640313, 34841674, 35911527, 34309407, 35103483, 37128929, 36860515, 36597672, 36693943, 38219013, 37324772, ZhangH2023[Abstract], 38254962, 36269083, 37614113, 38014677)

KCNH2: PP2, PP3, BS2

This variant has been reported in the following publications (PMID:10483966;PMID:10862094;PMID:14661677;PMID:16818214;PMID:17161064;PMID:19160088;PMID:19841300;PMID:19862833;PMID:16754261;PMID:22052944;PMID:22429796).