The etiologies of newborn deaths in neonatal intensive care units usually remain unknown, even following genetic testing. Whole-genome sequencing, combined with artificial intelligence-based methods for predicting the effects of non-coding variants, provide an avenue for resolving these deaths. Using one such method, SpliceAI, we identified a maternally inherited deep intronic PKHD1 splice variant (chr6:52030169T>C), in trans with a pathogenic missense variant (p.Thr36Met), in a baby who died of autosomal recessive polycystic kidney disease at age two days. We validated the deep intronic variant's impact in maternal urine-derived cells expressing PKHD1. Reverse transcription polymerase chain reaction followed by Sanger sequencing showed that the variant causes inclusion of 147bp of the canonical intron between exons 29 and 30 of PKHD1 into the mRNA, including a premature stop codon. Allele-specific expression analysis at a heterozygous site in the mother showed that the mutant allele completely suppresses canonical splicing. In an unrelated healthy control, there was no evidence of transcripts including the novel splice junction. We returned a diagnostic report to the parents, who underwent in vitro embryo selection.

Index words

SpliceAI, intronic, PKHD1, ARPKD, NICU, deceased

中文翻译：

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SpliceAI 在患有常染色体隐性多囊肾病的已故新生儿中鉴定出深内含子 PKHD1 变异

即使在进行基因检测后，新生儿重症监护病房新生儿死亡的病因通常仍不清楚。全基因组测序与基于人工智能的预测非编码变异影响的方法相结合，为解决这些死亡问题提供了一条途径。使用这样的方法 SpliceAI，我们在一名死于常染色体隐性多囊肾病的婴儿中鉴定出一种母系遗传的深部内含子PKHD1剪接变异体 (chr6:52030169T>C) ，该变异体与致病性错义变异体 (p.Thr36Met) 呈反式。年龄两天。我们验证了深部内含子变异对表达PKHD1 的母体尿液来源细胞的影响。逆转录聚合酶链反应和桑格测序表明，该变体导致PKHD1外显子 29 和 30 之间的 147bp 规范内含子包含到 mRNA 中，包括提前终止密码子。母亲杂合位点的等位基因特异性表达分析表明，突变等位基因完全抑制了规范剪接。在不相关的健康对照中，没有证据表明转录本包括新的剪接点。我们向接受体外胚胎选择的父母返回了一份诊断报告。

索引词

SpliceAI、intronic、PKHD1、ARPKD、NICU、已故