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）是一种严重的先天性异常，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立，但仅鉴定了少数疾病相关基因。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de novo编码变异，并证实了破坏性de novo变异的整体显着富集，尤其是在受限基因中。我们在de novo的基础上确定了LONP1（lon 肽酶 1，线粒体）和ALYREF（Aly/REF 输出因子）作为候选 CDH 相关基因错误发现率低于 0.05 的变异。我们还进行超罕见变异协会在748个受影响的个人和11,220血统相匹配的控制人口的个人和分析识别LONP1作为风险基因通过既有助于CDH从头在域的核心聚集和超罕见的遗传性在很大程度上杂变种并在受影响的家庭个体中与 CDH 隔离。在我们的 CDH 队列中，大约 3% 的具有LONP1中超罕见预测破坏性变异的杂合子具有一系列临床表型，包括某些个体的其他异常以及更高的死亡率和对体外膜氧合的要求。Lonp1肺上皮特异性缺失小鼠出生后立即死亡，很可能是因为观察到肺部生长严重减少，这是人类高死亡率的已知原因。我们对同一基因中的从头变异和遗传性罕见变异的发现可能对其他先天性异常的遗传研究的设计和分析产生影响。