PDF(Pubmed)
Abstract：
Pathogenic variants in the JAG1 gene are a primary cause of the multi-system disorder Alagille syndrome. Although variant detection rates are high for this disease, there is uncertainty associated with the classification of missense variants that leads to reduced diagnostic yield. Consequently, up to 85% of reported JAG1 missense variants have uncertain or conflicting classifications. We generated a library of 2,832 JAG1 nucleotide variants within exons 1-7, a region with a high number of reported missense variants, and designed a high-throughput assay to measure JAG1 membrane expression, a requirement for normal function. After calibration using a set of 175 known or predicted pathogenic and benign variants included within the variant library, 486 variants were characterized as functionally abnormal (n = 277 abnormal and n = 209 likely abnormal), of which 439 (90.3%) were missense. We identified divergent membrane expression occurring at specific residues, indicating that loss of the wild-type residue itself does not drive pathogenicity, a finding supported by structural modeling data and with broad implications for clinical variant classification both for Alagille syndrome and globally across other disease genes. Of 144 uncertain variants reported in patients undergoing clinical or research testing, 27 had functionally abnormal membrane expression, and inclusion of our data resulted in the reclassification of 26 to likely pathogenic. Functional evidence augments the classification of genomic variants, reducing uncertainty and improving diagnostics. Inclusion of this repository of functional evidence during JAG1 variant reclassification will significantly affect resolution of variant pathogenicity, making a critical impact on the molecular diagnosis of Alagille syndrome.
摘要：
JAG1基因中的致病变异是多系统疾病Alagille综合征的主要原因。尽管这种疾病的变异检出率很高，错义变异分类存在不确定性,导致诊断率降低.因此,高达85%的JAG1错义变异体分类不确定或相互矛盾.我们在外显子1-7中产生了2,832个JAG1核苷酸变体的文库，该区域具有大量报道的错义变体，并设计了一种高通量检测JAG1膜表达的方法，正常功能的要求。在使用变体文库中包含的175个已知或预测的致病性和良性变体的集合进行校准后，486个变体被表征为功能异常(n=277个异常和n=209个可能的异常)。其中439人(90.3%)是错误的。我们确定了在特定残基发生的不同膜表达，表明野生型残基的丢失本身不会驱动致病性，这一发现得到了结构模型数据的支持,对Alagille综合征和全球其他疾病基因的临床变异分类具有广泛意义.在接受临床或研究测试的患者中报告的144种不确定变异中，27例膜表达功能异常，纳入我们的数据导致26人重新分类为可能致病。功能证据增强了基因组变异的分类，减少不确定性并改善诊断。在JAG1变异体重新分类过程中包含此功能证据库将显着影响变异体致病性的分辨率，对Alagille综合征的分子诊断有重要影响。
