ClinVar Genomic variation as it relates to human health

PS3, PS4, PP1_Strong, PM2_Supporting, PM5, PP3, PP4

PM2, PP1, PP3, PM5, PP5, PP4

Reported in multiple individuals with LQTS and observed to segregate with disease (Splawski et al., 2000; Zareba et al., 2003; Kapplinger et al., 2009; Riuro et al., 2014; Yoshinaga et al.,2014; Jimenez-Jaimez et al., 2015; Kapplinger et al., 2015; Itoh et al., 2016; internal GeneDx data); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Functional analysis found that p.(R366Q) resulted in impaired subcellular trafficking of KCNQ1 channels to the plasma membrane (Wilson et al., 2005); This variant is associated with the following publications: (PMID: 32383558, 19934648, 14678125, 24363352, 26669661, 25854863, 24667783, 19716085, 25832545, 28472724, 22581653, 25804018, 29037160, 31737537, 34426522, 34860437, 35588786, 24689698, 15935335, 10973849)

Criteria: PS3_Moderate, PS4_Strong, PM1, PM2, PP3

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 366 of the KCNQ1 protein (p.Arg366Gln). This variant is present in population databases (rs199473410, gnomAD 0.0009%). This missense change has been observed in individuals with long QT syndrome, hearing loss and prolonged QTc (PMID: 14678125, 23158531, 24689698, 25804018, 26669661). ClinVar contains an entry for this variant (Variation ID: 52956). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt KCNQ1 protein function. Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 15935335, 19934648, 23861489). This variant disrupts the p.Arg366 amino acid residue in KCNQ1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9024139, 10973849, 15840476, 16556865, 22949429). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

KCNQ1: PM1, PM2, PM5, PS4:Moderate, PP3, PS3:Supporting

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.97; 3Cnet: 0.96). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000052956). Different missense changes at the same codon (p.Arg366Leu, p.Arg366Trp) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000052955 , VCV001185948). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

This missense variant replaces arginine with glutamine at codon 366 of the KCNQ1 protein. This variant is found within a highly conserved region (a.a.349-391) of the C-terminal cytoplasmic domain. Rare nontruncating variants in this region have been shown to be significantly overrepresented in individuals with long QT syndrome (PMID: 32893267). Functional studies have shown that this variant causes endoplasmic reticulum retention (PMID:15935335), affects the binding to phosphatidylinositol 4,5-bisphosphate (PIP2), results in decreased strength of PIP2-dependent coupling of the voltage-sensing domain and the pore domain and a reduction in channel current (PMID: 19934648, 23861489). This variant has been reported in over twenty families affected with long QT syndrome and more than half of them were from Turkish population (PMID: 10973849, 24363352, 24667783, 24689698, 25804018, 26669661, 28472724, 29037160, 32383558, 34860437). In these families, in addition to affected heterozygous carriers, this variant has also been observed in homozygous state in multiple individuals affected with long QT syndrome and congenital hearing loss (PMID: 34860437), in compound heterozygous state with a pathogenic splice variant in an individual affected with Jervell and Lange-Nielsen syndrome (PMID: 32383558), and in digenic heterozygous state with a known pathogenic SCN5A variant in an individual diagnosed with long QT syndrome at a young age (PMID: 25804018). This variant has been identified in 1/251240 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

GENETIC TEST RESULTS Our patient has a clinical phenotype of LQTS, with QTc interval of >500 msec on some EKGs. She had genetic testing for LQTS with the Invitae laboratory. The following 17 genes were evaluated for sequence changes and exonic deletions/duplications: AKAP9, ANK2, CACNA1C, CALM1, CALM2, CALM3, CAV3, KCNE1, KCNE2, KCNH2, KCNJ2, KCNJ5, KCNQ1, SCN4B, SCN5A, SNTA1, TRDN. Results showed two variants: • p.Arg366Gln (R366Q; c.1097G>A) in the KCNQ1 gene (diagnostic of LQTS type 1) • p.Ile688Asn (I688N; c.2063T>A) in the ANK2 gene p.Arg366Gln (R366Q; c.1097G>A) in exon 8 of the KCNQ1 gene (NM_000218.2) Chromosome location: 11:2606506 G / A Invitae classifies Arg366Gln as Pathogenic. Based on the information reviewed below, including multiple reports in well-phenotyped patients in the literature, strong segregation data, and a near absence from population datasets, we classify it as Very Likely Disease Causing, concluding that there is sufficient evidence for its pathogenicity to warrant using it for diagnosis of long QT syndrome type 1 (LQT1) and predictive genetic testing. This variant has previously been reported multiple times, in approximately 7 unrelated families with LQTS. Other variants at this same amino acid have also been reported multiple times in LQTS patients. Zareba et al. (2003; PMID 14678125) reported it in 2 individuals with LQT1 from the International LQTS Registry (it is possible that they are related). They also reported a different amino acid change, Arg366Trp, at this same codon in one patient. Crotti et al. reported it in 2 individuals with LQTS from 2 families (2012; PMID 23158531); these cases may overlap with the Zareba cases. Itoh et al. (2016; PMID 26669661) reported it in 3 separate LQTS families, and also reported Arg366Trp in 5 families and Arg366Pro in one family. Ertugrul et al. (2014; PMID 25804018) reported it in a LQTS patient who also had a variant in SCN5A. Strong segregation data is available: Tekin et al. reported it in homozygous form in a deaf Turkish brother and sister each with Jervell and Lange-Nielsen syndrome (2014; PMID 24689698), and confirmed that both of their hearing parents were heterozygous. One of the other missense substitutions at this codon (p.Arg366Trp) has been reported to ClinVar as Pathogenic by both GeneDx and Invitae, further suggesting that the p.Arg366 residue is important for KCNQ1 protein function. Other missense variants +/- 5 amino acids have also been submitted to ClinVar as disease-causing. According to the Invitae report: Experimental studies have shown that this missense variant decreases the affinity of the KCNQ1 protein for PIP2, reducing the channel current amplitude. This variant has also been reported to lead to subcellular mislocalization of the KCNQ1 protein (PMID: 15935335, 19934648 , 23861489). We did not review this literature. This is a nonconservative amino acid change, resulting in the replacement of a positively-charged Arginine with a polar Glutamine. Residue 366 is in the cytoplasmic C-terminal domain of the protein (residues 349-676), in which missense variants are 22x more frequent in LQTS cases than in controls (Kapa et al. 2009). Arginine at this location is absolutely conserved across ~80 vertebrate species for which we have data. The surrounding residues are also absolutely conserved. This variant was reported in 1 non-Finnish European individual in the gnomAD database, which includes variant calls on ~140,000 individuals of European, African, Latino, South Asian, Ashkenazi, and East Asian descent. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. The curators made an effort to exclude individuals with severe pediatric diseases. No individual with p.Arg366Trp or p.Arg366Pro currently appears in gnomAD.

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:10973849;PMID:14678125;PMID:19716085;PMID:19934648;PMID:15935335). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.