ClinVar Genomic variation as it relates to human health

The D837G pathogenic variant in the KCNH2 gene has been reported previously in association with LQTS, and this variant was absent from 1,488 control alleles (Khositseth et al., 2004; Tester et al., 2005; Partemi et al., 2014). In addition, the NHLBI Exome Sequencing Project reports D837G was not observed in approximately 6,500 samples from individuals of European and African American backgrounds, indicating it is not a common benign variant in these populations. The D837G variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution also occurs at a position that is conserved across species and islocated in the cyclic-nucleotide-binding homology domain (CNBHD). Moreover, functional studies have shown that variants in the CNBHD can cause incorrect folding that can lead to protein instability and ultimately deficient protein trafficking (Li et al., 2016; Anderson et al., 2014). Furthermore, pathogenic missense variants at the same residue (D837N, D837Y), as well as variants in nearby residues (R835W, R835Q, V841L, P846S, P846T) have been reported in association with LQTS (Stenson et al., 2014), supporting the functional importance of this region of the protein. In summary, D837G in the KCNH2 gene is interpreted as a pathogenic variant.

Variant summary: KCNH2 c.2510A>G (p.Asp837Gly) results in a non-conservative amino acid change located in the Cyclic nucleotide-binding domain (IPR000595) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251458 control chromosomes (gnomAD). c.2510A>G has been reported in the literature in individuals with personal and family history of Arrhythmia (Khositseth_2004, Tester_2005, Mullally_2013, Lieve_2013, Partemi_2015). These data indicate that the variant may be associated with disease. To our knowledge, two publications have shown experimental evidence that the variant impacts protein function: the variant induces a trafficking defect of the mature hERG channel when expressed alone in HEK293 cells, and in a dominant-negative manner when co-expressed with wild-type protein (Anderson_2014). Conformational changes that were detected via NMR spectrometry in E.coli purified protein have been suggested as a cause of this deficiency (Li_2016). Four ClinVar submitters have assessed this variant since 2014: three classified the variant as likely pathogenic, and one as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

The KCNH2 c.2510A>G; p.Asp837Gly variant (rs199473004) is reported in the literature in several individuals affected with long QT syndrome (Lieve 2013, Migdalovich 2011, Mullally 2013, Partemi 2015, Tester 2005). This variant is also reported in ClinVar (Variation ID: 67407), but is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The aspartate at codon 837 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.959). Functional analyses of the variant protein show abnormal trafficking and gating (Anderson 2014). Additionally, other amino acid substitutions at this codon (Tyr, Asn, His) have been reported in individuals with long QT syndrome (Kapa 2009, Kapplinger 2009, Robyns 2017). Based on available information, this variant is considered to be likely pathogenic. References: Anderson CL et al. Large-scale mutational analysis of Kv11.1 reveals molecular insights into type 2 long QT syndrome. Nat Commun. 2014 Nov 24;5:5535. PMID: 25417810. Kapa S et al. Genetic testing for long-QT syndrome: distinguishing pathogenic mutations from benign variants. Circulation. 2009 Nov 3;120(18):1752-60. PMID: 19841300. Kapplinger JD et al. Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Heart Rhythm. 2009 Sep;6(9):1297-303. PMID: 19716085. Lieve KV et al. Results of genetic testing in 855 consecutive unrelated patients referred for long QT syndrome in a clinical laboratory. Genet Test Mol Biomarkers. 2013 Jul;17(7):553-61. PMID: 23631430. Migdalovich D et al. Mutation and gender-specific risk in type 2 long QT syndrome: implications for risk stratification for life-threatening cardiac events in patients with long QT syndrome. Heart Rhythm. 2011 Oct;8(10):1537-43. PMID: 21440677. Mullally J et al. Risk of life-threatening cardiac events among patients with long QT syndrome and multiple mutations. Heart Rhythm. 2013 Mar;10(3):378-82. PMID: 23174487. Partemi S et al. Genetic and forensic implications in epilepsy and cardiac arrhythmias: a case series. Int J Legal Med. 2015 May;129(3):495-504. PMID: 25119684. Robyns T et al. Individualized corrected QT interval is superior to QT interval corrected using the Bazett formula in predicting mutation carriage in families with long QT syndrome. Heart Rhythm. 2017 Mar;14(3):376-382. PMID: 28212739. Tester DJ et al. Compendium of cardiac channel mutations in 541 consecutive unrelated patients referred for long QT syndrome genetic testing. Heart Rhythm. 2005 May;2(5):507-17. PMID: 15840476.

This variant is interpreted as a Likely Pathogenic, for Long QT syndrome 2, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PS3-Moderate => PS3 downgraded in strength to Moderate. PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS4-Moderate => Mutation found in multiple unrelated patients and absent from population databases.

This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 837 of the KCNH2 protein (p.Asp837Gly). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of long QT syndrome (PMID: 21440677, 25119684; Invitae). ClinVar contains an entry for this variant (Variation ID: 67407). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects KCNH2 function (PMID: 25417810). This variant disrupts the p.Asp837 amino acid residue in KCNH2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 19841300, 26669661). 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.

The c.2510A>G (p.Asp837Gly) variant in the KCNH2 gene is predicted to replace aspartic acid with glycine at codon 837 (p.Asp837Gly). This variant has been reported in multiple individuals with long QT syndrome (PMID: 21440677, 15851119, 25119684, 20850565, 23631430). Experimental analysis of the variant in cultured cell line proved the deficient protein trafficking and the negative functional impact (PMID: 25417810). Alternative variants disrupting the same amino acid (p.Asp837Asn, p.Asp837Tyr) have been interpreted as pathogenic/likely pathogenic (ClinVar ID: 67405, 67406). The variant is reported in ClinVar (ID: 67407). The variant is absent in the general population database (gnomAD). Computational prediction algorithms suggest a deleterious impact for this variant (REVEL score 0.959). Therefore, the c.2510A>G (p.Asp837Gly) variant of KCNH2 has been classified as likely pathogenic.

The p.D837G variant (also known as c.2510A>G), located in coding exon 10 of the KCNH2 gene, results from an A to G substitution at nucleotide position 2510. The aspartic acid at codon 837 is replaced by glycine, an amino acid with similar properties, and is located in the cyclic nucleotide binding region of the protein. This variant has been reported in individuals with long QT syndrome (Khositseth A et al. Heart Rhythm. 2004;1(1):60-4; Ambry internal data). Immunoblot data suggest that this variant is a protein trafficking deficient alteration (Anderson CL et al. Nat Commun. 2014;5:5535). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:15840476;PMID:15851119). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory.