Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA.
Medical Scientist Training Program, Vanderbilt University, Nashville, TN, 37232, USA.
Genome Med. 2024 May 30;16(1):73. doi: 10.1186/s13073-024-01340-5.
KCNE1 encodes a 129-residue cardiac potassium channel (I) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility.
In this study, we leveraged the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein-coding KCNE1 variants.
We comprehensively assayed KCNE1 variant cell surface expression (2554/2709 possible single-amino-acid variants) and function (2534 variants). Our study identified 470 loss- or partial loss-of-surface expression and 574 loss- or partial loss-of-function variants. Of the 574 loss- or partial loss-of-function variants, 152 (26.5%) had reduced cell surface expression, indicating that most functionally deleterious variants affect channel gating. Nonsense variants at residues 56-104 generally had WT-like trafficking scores but decreased functional scores, indicating that the latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation (with > 70% loss-of-function variants) were in predicted close contact with binding partners KCNQ1 or calmodulin. Our functional assay data were consistent with gold standard electrophysiological data (ρ = - 0.64), population and patient cohorts (32/38 presumed benign or pathogenic variants with consistent scores), and computational predictors (ρ = - 0.62). Our data provide moderate-strength evidence for the American College of Medical Genetics/Association of Molecular Pathology functional criteria for benign and pathogenic variants.
Comprehensive variant effect maps of KCNE1 can both provide insight into I channel biology and help reclassify variants of uncertain significance.
KCNE1 编码一个由 129 个氨基酸残基组成的心肌钾通道（I）亚基。KCNE1 变体与长 QT 综合征和心房颤动有关。然而，大多数变体缺乏临床后果的充分证据，因此临床应用有限。
在这项研究中，我们利用变体效应作图的力量，将饱和诱变与高通量测序相结合，确定数千种 KCNE1 变体的功能。
我们全面检测了 KCNE1 变体的细胞表面表达（2709 个可能的单个氨基酸变体中的 2554 个）和功能（2534 个变体）。我们的研究鉴定了 470 个缺失或部分缺失细胞表面表达和 574 个缺失或部分缺失功能的变体。在 574 个缺失或部分缺失功能的变体中，有 152 个（26.5%）细胞表面表达减少，表明大多数功能上有害的变体影响通道门控。残基 56-104 处的无意义变体通常具有 WT 样转运评分，但功能评分降低，表明蛋白后半段对于蛋白转运是可有可无的，但对于通道功能是必需的。在 30 个 KCNE1 残基中（73%），22 个高度耐受变异（有超过 70%的功能缺失变体）的残基位于与结合伴侣 KCNQ1 或钙调蛋白预测的紧密接触处。我们的功能测定数据与金标准电生理数据（ρ=−0.64）、人群和患者队列（32/38 个假定良性或致病性变体具有一致的评分）以及计算预测因子（ρ=−0.62）一致。我们的数据为美国医学遗传学学院/分子病理学协会良性和致病性变体的功能标准提供了中等强度的证据。
KCNE1 的综合变体效应图谱既能深入了解 I 通道生物学，又能帮助重新分类不确定意义的变体。
