We investigated the genetic origin of the phenotype displayed by three children from two unrelated Italian families, presenting with a previously unrecognized autosomal recessive disorder that included a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability and Leber congenital amaurosis (SHILCA), as well as some brain anomalies that were visible at the MRI. Autozygome-based analysis showed that these children shared a 4.76 Mb region of homozygosity on chromosome 1, with an identical haplotype. Nonetheless, whole-exome sequencing failed to identify any shared rare coding variants, in this region or elsewhere. We then determined the transcriptome of patients’ fibroblasts by RNA sequencing, followed by additional whole-genome sequencing experiments. Gene expression analysis revealed a 4-fold downregulation of the gene NMNAT1, residing indeed in the shared autozygous interval. Short- and long-read whole-genome sequencing highlighted a duplication involving 2 out of the 5 exons of NMNAT1 main isoform (NM_022787.3), leading to the production of aberrant mRNAs. Pathogenic variants in NMNAT1 have been previously shown to cause non-syndromic Leber congenital amaurosis (LCA). However, no patient with null biallelic mutations has ever been described, and murine Nmnat1 knockouts show embryonic lethality, indicating that complete absence of NMNAT1 activity is probably not compatible with life. The rearrangement found in our cases, presumably causing a strong but not complete reduction of enzymatic activity, may therefore result in an intermediate syndromic phenotype with respect to LCA and lethality.

中文翻译：

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Alu 介导的 NMNAT1 重复，参与 NAD 生物合成，导致一种新的综合征，SHILCA，影响多个组织和器官。

我们研究从两个不相干的意大利家庭的三个孩子中显示的表型的遗传起源，与先前未知的常染色体隐性遗传疾病，包括严重形式呈现小号pondylo骨骺发育不良，感觉^ h抽穗损失，我ntellectual残疾和大号希伯Ç ongenital一maurosis (SHILCA)，以及在 MRI 中可见的一些大脑异常。基于自合子组的分析表明，这些孩子在 1 号染色体上共享一个 4.76 Mb 的纯合子区域，具有相同的单倍型。尽管如此，全外显子组测序未能在该区域或其他地方识别出任何共享的罕见编码变异。然后，我们通过 RNA 测序确定了患者成纤维细胞的转录组，然后进行了额外的全基因组测序实验。基因表达分析揭示了基因NMNAT1的 4 倍下调，确实存在于共享的自合子区间。短读长和长读长全基因组测序突出显示了涉及NMNAT1 5 个外显子中的 2 个的重复主要同种型 (NM_022787.3)，导致异常 mRNA 的产生。NMNAT1 中的致病变异先前已被证明会导致非综合征性 Leber 先天性黑蒙 (LCA)。然而，从未描述过具有无效双等位基因突变的患者，并且小鼠Nmnat1敲除显示胚胎致死率，表明完全缺乏 NMNAT1 活性可能与生命不相容。在我们的病例中发现的重排可能导致酶活性强烈但未完全降低，因此可能导致 LCA 和致死率方面的中间综合征表型。