Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota.
Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology & Experimental Therapeutics, Windland Smith Rice Sudden Death Genomics Laboratory, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Division of Heart Rhythm Services, Mayo Clinic, Rochester, Minnesota.
Heart Rhythm. 2020 Feb;17(2):315-323. doi: 10.1016/j.hrthm.2019.08.014. Epub 2019 Sep 5.
Loss-of-function variants in the KCNH2-encoded Kv11.1 potassium channel cause long QT syndrome (LQTS) type 2 (LQT2). Presently, hundreds of KCNH2 missense variants (MVs) have been published as "disease-causative." However, an estimated 10% of rare published LQTS MVs may be "false positives."
The purpose of this study was to determine which published KCNH2 MVs are likely false positives and warrant demotion to "likely benign" status.
A list of 337 LQT2-associated MVs from 6 large compendia was compiled. MV frequency within the Genome Aggregation Database (gnomAD) (n = 141,352 individuals) was assessed, and MVs were analyzed with 8 in silico tools. Variants with minor allele frequency (MAF) >7*10E-6, the calculated maximum credible frequency of LQT2, and predicted "benign" by all tools were demoted to "likely benign." Ultra-rare variants (n = 8) absent in gnomAD but predicted "benign" by all tools were considered as potential false positives and were characterized functionally using whole-cell patch clamp.
Overall, 14 of 337 published KCNH2 MVs (4%) were observed at MAF >7*10E-6, whereas 252 of 337 (75%) were absent in gnomAD. Among the latter, 8 variants (I96V, G187S, A203T, P241L, H254Q, G314S, P935S, P963T) were predicted benign by 8 tools and lacked characterization. Patch clamp showed no functional perturbation for these 8 MVs.
This study offers compelling evidence for the demotion of 22 of 337 KCNH2 variants (6.5%) in the literature. Meticulous "pruning" of compendia using exome/genome databases, in silico tools, and in vitro functional studies must be conducted not only for putatively pathogenic LQTS MVs but for the entire field of genetic heart disease.
编码 Kv11.1 钾通道的 KCNH2 基因中的功能丧失性变异会导致长 QT 综合征（LQTS）型 2（LQT2）。目前，已有数百种 KCNH2 错义变异（MV）被发表为“致病”。然而，估计有 10%的罕见发表的 LQTS MV 可能是“假阳性”。
本研究旨在确定哪些已发表的 KCNH2 MV 可能是假阳性，并将其降级为“可能良性”状态。
编制了来自 6 个大型汇编的 337 个 LQT2 相关 MV 的列表。在基因组聚集数据库（gnomAD）（n=141352 人）中评估 MV 频率，并使用 8 种计算工具分析 MV。将等位基因频率（MAF）>710E-6、计算出的 LQT2 的最大可信频率和所有工具预测的“良性”的变异降为“可能良性”。MAF>710E-6 的罕见变异（n=8）在 gnomAD 中不存在，但所有工具均预测为“良性”，则被认为是潜在的假阳性，并使用全细胞膜片钳进行功能表征。
总体而言，在 337 个已发表的 KCNH2 MV 中，有 14 个（4%）的 MAF>7*10E-6，而 337 个中有 252 个（75%）在 gnomAD 中缺失。在后者中，8 个变异（I96V、G187S、A203T、P241L、H254Q、G314S、P935S、P963T）被 8 种工具预测为良性，且缺乏特征。膜片钳对这 8 个 MV 没有显示出功能扰动。
本研究为降级文献中 337 个 KCNH2 变异中的 22 个（6.5%）提供了有力的证据。使用外显子/基因组数据库、计算工具和体外功能研究，对包含可能致病的 LQTS MV 在内的整个遗传性心脏病领域进行仔细的“修剪”是必要的。
