Abstract：
Whole-exome sequencing (WES) is an excellent method for the diagnosis of diseases of uncertain or heterogeneous genetic origin. However, it has limitations for detecting structural variations such as InDels, which the bioinformatics analyzers must be aware of. This study aimed at using WES to evaluate the genetic cause of the metabolic crisis in a 3-day-old neonate admitted to the neonatal intensive care unit (NICU) and deceased after a few days. Tandem mass spectrometry (MS/MS) showed a significant increase in propionyl carnitine (C3), proposing methylmalonic acidemia (MMA) or propionic acidemia (PA). WES demonstrated a homozygous missense variant in exon 4 of the BTD gene (NM_000060.4(BTD):c.1330G > C), responsible for partial biotinidase deficiency. Segregation analysis of the BTD variant revealed the homozygous status of the asymptomatic mother. Furthermore, observation of the bam file, around genes responsible for PA or MMA, by Integrative Genomics Viewer (IGV) software displayed a homozygous large deletion in the PCCA gene. Comprehensive confirmatory studies identified and segregated a novel outframe deletion of 217,877 bp length, \"NG_008768.1:g.185211_403087delinsTA\", extended from intron 11 to 21 of the PCCA, inducing a premature termination codon and activation of nonsense-mediated mRNA decay (NMD). Homology modeling of the mutant PCCA demonstrated eliminating the protein\'s active site and critical functional domains. Thereupon, this novel variant is suggested as the largest deletion in the PCCA gene, causing an acute early-onset PA. These results could expand the PCCA variants spectrum, and improve the existing knowledge on the molecular basis of PA, as well as provide new evidence of pathogenicity of the variant (NM_000060.4(BTD):c.1330G > C.
摘要：
全外显子组测序（WES）是诊断遗传起源不确定或异质性疾病的理想方法。然而,它在检测诸如InDels之类的结构变化方面具有局限性，生物信息学分析仪必须意识到这一点。这项研究旨在使用WES评估3天大的新生儿进入新生儿重症监护病房（NICU）并在几天后死亡的代谢危机的遗传原因。串联质谱（MS/MS）显示丙酰基肉碱（C3）的显着增加，提出甲基丙二酸血症（MMA）或丙酸血症（PA）。WES在BTD基因的外显子4中表现出纯合错义变异(NM_000060.4(BTD):c.1330G>C),负责部分生物素酶缺乏症。BTD变体的分离分析揭示了无症状母亲的纯合状态。此外，观察BAM档案,围绕负责PA或MMA的基因，通过整合基因组学查看器（IGV）软件显示PCCA基因中的纯合大缺失。综合验证性研究确定并分离了一个新的217,877bp长度的外框缺失，\"NG_008768.1:g.185211_403087delinsTA\",从PCCA的内含子11延伸到21，诱导过早终止密码子和激活无义介导的mRNA衰变（NMD）。突变体PCCA的同源性建模表明消除了蛋白质的活性位点和关键功能域。于是,这种新的变异被认为是PCCA基因中最大的缺失，导致急性早发性PA。这些结果可以扩展PCCA变体谱，并在PA的分子基础上改进现有知识，以及提供该变异体致病性的新证据(NM_000060.4(BTD):c.133G>C.
