Biallelic pathogenic variants in SZT2 result in a neurodevelopmental disorder with shared features, including early-onset epilepsy, developmental delay, macrocephaly, and corpus callosum abnormalities. SZT2 is as a critical scaffolding protein in the amino acid sensing arm of the mTORC1 signalling pathway. Due to its large size (3432 amino acids), lack of crystal structure, and absence of functional domains, it is difficult to determine the pathogenicity of SZT2 missense and in-frame deletions, but these variants are increasingly detected and reported by clinical genetic testing in individuals with epilepsy. To exemplify this latter point, here we describe a cohort of 12 individuals with biallelic SZT2 variants and phenotypic overlap with SZT2-related neurodevelopmental disorders. However, the majority of individuals carried one or more SZT2 variants of uncertain significance (VUS), highlighting the need for functional characterization to determine, which, if any, of these VUS were pathogenic. Thus, we developed a novel individualized platform to identify SZT2 loss-of-function variants in the context of mTORC1 signalling and reclassify VUS. Using this platform, we identified a recurrent in-frame deletion (SZT2 p.Val1984del) which was determined to be a loss-of-function variant and therefore likely pathogenic. Haplotype analysis revealed that this single in-frame deletion is a founder variant in those of Ashkenazi Jewish ancestry. Moreover, this approach allowed us to tentatively reclassify all of the VUS in our cohort of 12 individuals, identifying five individuals with biallelic pathogenic or likely pathogenic variants. Clinical features of these five individuals consisted of early-onset seizures (median 24 months), focal seizures, developmental delay and macrocephaly similar to previous reports. However, we also show a widening of the phenotypic spectrum, as none of the five individuals had corpus callosum abnormalities, in contrast to previous reports. Overall, we present a rapid assay to resolve VUS in SZT2, identify a founder variant in individuals of Ashkenazi Jewish ancestry, and demonstrate that corpus callosum abnormalities is not a hallmark feature of this condition. Our approach is widely applicable to other mTORopathies including the most common causes of the focal genetic epilepsies, DEPDC5, TSC1/2, MTOR and NPRL2/3.

中文翻译：

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mTORC1 功能测定揭示了 SZT2 功能丧失变异和创始人框内删除。


SZT2 的双等位基因致病性变异会导致具有共同特征的神经发育障碍，包括早发性癫痫、发育迟缓、大头畸形和胼胝体异常。 SZT2 是 mTORC1 信号通路氨基酸传感臂中的关键支架蛋白。由于其体积大（3432个氨基酸）、缺乏晶体结构和缺乏功能域，很难确定SZT2错义和框内缺失的致病性，但这些变异越来越多地被临床基因检测检测和报告癫痫患者。为了举例说明后一点，我们在这里描述了一组 12 名具有双等位基因 SZT2 变异且与 SZT2 相关神经发育障碍表型重叠的个体。然而，大多数个体携带一种或多种意义不确定的 SZT2 变异 (VUS)，这突出表明需要进行功能表征来确定这些 VUS 中哪些（如果有）具有致病性。因此，我们开发了一个新颖的个性化平台来识别 mTORC1 信号传导背景下的 SZT2 功能丧失变异并重新分类 VUS。使用该平台，我们鉴定了一个反复出现的框内缺失（SZT2 p.Val1984del），该突变被确定为功能丧失性变异，因此可能具有致病性。单倍型分析表明，这种单一的框内缺失是德系犹太人血统中的一个创始变体。此外，这种方法使我们能够对 12 名个体中的所有 VUS 进行初步重新分类，识别出 5 名具有双等位基因致病变异或可能致病变异的个体。 这 5 个人的临床特征包括早发性癫痫发作（中位 24 个月）、局灶性癫痫发作、发育迟缓和巨头畸形，与之前的报告类似。然而，我们也显示出表型谱的扩大，因为与之前的报告相比，这五个人都没有胼胝体异常。总体而言，我们提出了一种快速检测方法来解决 SZT2 中的 VUS，识别德系犹太人血统个体中的创始人变异，并证明胼胝体异常不是这种情况的标志特征。我们的方法广泛适用于其他 mTORopathies，包括局灶性遗传性癫痫的最常见原因、DEPDC5、TSC1/2、MTOR 和 NPRL2/3。