Abstract Prolidase Deficiency (PD) is an autosomal recessive rare disorder caused by loss or reduction of prolidase enzymatic activity due to variants in the PEPD gene. PD clinical features vary among affected individuals: skin ulcerations, recurrent infections, and developmental delay are common. In this study, we describe a 16-year-old boy with a mild PD phenotype comprising chronic eczema, recurrent infections and elevated IgE. Whole exome sequencing analysis revealed three PEPD variants: c.575T>C p.(Leu192Pro) inherited from the mother, and c.692_694del p.(Tyr231del) and c.1409G>A p.(Arg470His), both inherited from the father. The variant p.(Tyr231del) has been previously characterized by high-resolution X-ray structure analysis as altering protein dynamics/flexibility. In order to study the effects of the other two prolidase variants, we performed site directed mutagenesis purification and crystallization studies. A high-resolution X-ray structure could only be obtained for the p.(Arg470His) variant, which showed no significant structural differences in comparison to WT prolidase. On the other hand, the p.(Leu192Pro) variant led to significant protein destabilization. Hence, we conclude that the maternal p.(Leu192Pro) variant was likely causally associated with the proband´s disease, together with the known pathogenic paternal variant p.(Tyr231del). Our results demonstrated the utility of exome sequencing to perform diagnosis in PD cases with mild phenotype.

中文翻译：

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通过外显子组测序诊断患有脯氨酸酶缺乏症的患者中鉴定的PEPD基因新复合杂合变体的结构分析

摘要脯氨酸蛋白酶缺乏症（PD）是一种常染色体隐性遗传性罕见疾病，由PEPD基因变异引起的脯氨酸酶酶活性丧失或降低引起。PD的临床特征在受影响的个体之间有所不同：皮肤溃疡，反复感染和发育迟缓很常见。在这项研究中，我们描述了一个16岁的男孩，患有轻度的PD表型，包括慢性湿疹，反复感染和IgE升高。整个外显子组测序分析显示了三种PEPD变体：从母亲继承的c.575T> C p。（Leu192Pro），以及从父亲遗传的c.692_694del p。（Tyr231del）和c.1409G> A p。（Arg470His） 。变体p。（Tyr231del）先前已通过高分辨率X射线结构分析表征为改变蛋白质动力学/灵活性。为了研究其他两种蛋白水解酶变体的作用，我们进行了定点诱变纯化和结晶研究。仅对于p。（Arg470His）变体可以获得高分辨率的X射线结构，与WT脯氨酸蛋白酶相比，该变体没有显着的结构差异。另一方面，p。（Leu192Pro）变体导致明显的蛋白质不稳定。因此，我们得出结论，母体p。（Leu192Pro）变体可能与先证者疾病以及已知的致病性父系变体p。（Tyr231del）因果相关。我们的结果证明了外显子组测序在具有轻度表型的PD病例中进行诊断的实用性。与野生型脯氨酸蛋白酶相比，它没有显示出明显的结构差异。另一方面，p。（Leu192Pro）变体导致明显的蛋白质不稳定。因此，我们得出结论，母体p。（Leu192Pro）变体可能与先证者疾病以及已知的致病性父系变体p。（Tyr231del）因果相关。我们的结果证明了外显子组测序在具有轻度表型的PD病例中进行诊断的实用性。与野生型脯氨酸蛋白酶相比，它没有显示出明显的结构差异。另一方面，p。（Leu192Pro）变体导致明显的蛋白质不稳定。因此，我们得出结论，母体p。（Leu192Pro）变体可能与先证者疾病以及已知的致病性父系变体p。（Tyr231del）因果相关。我们的结果证明了外显子组测序在具有轻度表型的PD病例中进行诊断的实用性。