High throughput DNA sequencing is increasingly employed to diagnose single gene neurological and neuromuscular disorders. Large volumes of data present new challenges in data interpretation and its useful translation into clinical and genetic counselling for families. Even when a plausible gene is identified with confidence, interpretation of the clinical significance and inheritance pattern of variants can be challenging. We report our approach to evaluating variants in the skeletal muscle chloride channel ClC-1 identified in 223 probands with myotonia congenita (MC) as an example of these challenges. Sequencing of CLCN1, the gene that encodes CLC-1, is central to the diagnosis of MC. However, interpreting the pathogenicity and inheritance pattern of novel variants is notoriously difficult as both dominant and recessive mutations are reported throughout the channel sequence, ClC-1 structure-function is poorly understood and significant intra- and interfamilial variability in phenotype is reported. Heterologous expression systems to study functional consequences of CIC-1 variants are widely reported to aid the assessment of pathogenicity and inheritance pattern. However, heterogeneity of reported analyses does not allow for the systematic correlation of available functional and genetic data. We report the systematic evaluation of 95 CIC-1 variants in 223 probands, the largest reported patient cohort, in which we apply standardised functional analyses and correlate this with clinical assessment and inheritance pattern. Such correlation is important to determine if functional data improves the accuracy of variant interpretation and likely mode of inheritance. Our data provide an evidence-based approach that functional characterisation of ClC-1 variants improves clinical interpretation of their pathogenicity and inheritance pattern and serve as reference for 34 previously unreported and 28 previously uncharacterised CLCN1 variants. In addition, we identify novel pathogenic mechanisms and find that variants that alter voltage dependence of activation cluster in the first half of the transmembrane domains and variants that yield no currents cluster in the second half of the transmembrane domain. None of the variants in the intracellular domains were associated with dominant functional features or dominant inheritance pattern of MC. Our data help provide an initial estimate of the anticipated inheritance pattern based on the location of a novel variant and shows that systematic functional characterisation can significantly refine the assessment of risk of an associated inheritance pattern and consequently the clinical and genetic counselling.

中文翻译：

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将遗传和功能数据转化为临床实践：223 个肌强直家庭的系列研究


高通量 DNA 测序越来越多地用于诊断单基因神经和神经肌肉疾病。大量数据对数据解释及其有效转化为家庭临床和遗传咨询提出了新的挑战。即使可靠地鉴定了一个看似合理的基因，对变异的临床意义和遗传模式的解释也可能具有挑战性。我们报告了评估 223 名先天性肌强直 (MC) 先证者中鉴定的骨骼肌氯离子通道 ClC-1 变异的方法，作为这些挑战的一个例子。 CLCN1（编码 CLC-1 的基因）的测序对于 MC 的诊断至关重要。然而，解释新变异的致病性和遗传模式非常困难，因为在整个通道序列中都报道了显性和隐性突变，对 ClC-1 结构功能了解甚少，并且报道了显着的家族内和家族间表型变异。研究 CIC-1 变体功能后果的异源表达系统被广泛报道，以帮助评估致病性和遗传模式。然而，报告分析的异质性不允许现有功能和遗传数据的系统相关性。我们报告了对 223 个先证者（报告的最大的患者队列）中 95 个 CIC-1 变异的系统评估，其中我们应用标准化功能分析并将其与临床评估和遗传模式相关联。这种相关性对于确定功能数据是否提高变异解释和可能的遗传模式的准确性非常重要。 我们的数据提供了一种基于证据的方法，即 ClC-1 变体的功能表征改善了对其致病性和遗传模式的临床解释，并为 34 个先前未报告的 CLCN1 变体和 28 个先前未表征的 CLCN1 变体提供了参考。此外，我们还确定了新的致病机制，并发现改变激活电压依赖性的变体聚集在跨膜域的前半部分，而不产生电流的变体聚集在跨膜域的后半部分。胞内结构域中的变异均与 MC 的显性功能特征或显性遗传模式无关。我们的数据有助于根据新变异的位置提供对预期遗传模式的初步估计，并表明系统的功能表征可以显着改进对相关遗传模式风险的评估，从而改进临床和遗传咨询。