Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.

先天性膈疝（CDH）是一种严重的先天异常，通常伴有其他异常。尽管遗传学在 CDH 发病机制中的作用已经确定，但仅鉴定了少量疾病相关基因。为了进一步研究 CDH 的遗传学，我们分析了 827 个先证者父母三人组中的从头编码变异，并证实了破坏性从头变异的整体显着富集，特别是在受限基因中。我们基于de novo变异，以低于 0.05 的错误发现率，将LONP1 （lon 肽酶 1，线粒体）和ALYREF （Aly/REF 输出因子）确定为候选 CDH 相关基因。我们还在 748 名受影响个体和 11,220 名血统匹配的群体对照个体中进行了超罕见变异关联分析，并通过聚集在域核心的从头变异和超罕见遗传性杂合变异，将LONP1确定为导致 CDH 的风险基因。并在受影响的家族个体中与 CDH 进行隔离。我们的 CDH 队列中大约 3% 的杂合子具有LONP1中极其罕见的预测破坏性变异，具有一系列临床表型，包括一些个体的其他异常以及更高的死亡率和体外膜氧合的需要。肺上皮特异性缺失Lonp1的小鼠在出生后立即死亡，很可能是因为观察到肺生长严重减少，这是人类高死亡率的已知原因。 我们对同一基因的从头变异和遗传性罕见变异的发现可能对先天性异常的其他遗传研究的设计和分析具有影响。