Abstract Variant annotations are crucial for the efficient identification of pathogenic variants. In this study, we retrospectively evaluated the impact of various annotations on identifying 273 pathogenic single nucleotide and small insertion/deletion variants (SNVs/small indels) from 242 patients. Although variant filtering based on allele frequency is essential for narrowing down candidate variants, we found that 13 de novo pathogenic variants in autosomal dominant or X-linked dominant genes had been registered in gnomADv4.0 or 54KJPN with an allele frequency of less than 0.001%, suggesting that very rare variants in large cohort data can be pathogenic de novo variants. Strikingly, 38.1% candidate SNVs/small indels had been registered in the ClinVar database as pathogenic or likely pathogenic, highlighting great utility of this database. SpliceAI can detect candidate variants affecting RNA splicing, leading to the identification of four variants located at 11 to 50-bp away from the exon-intron boundary. Prioritization of candidate genes by patients’ phenotypes using PhenoMatcher module revealed that approximately 95% of the candidate genes had a maximum PhenoMatch score of ≥ 0.6, suggesting the utility of variant prioritization using phenotypes. This study suggests that a combination of multiple annotations and the appropriate evaluation can improve the diagnostic yield of rare diseases.
Vici syndrome is an autosomal recessive disorder involving autophagy dysfunction caused by the biallelic pathogenic variants in ectopic P-granules 5 autophagy tethering factor (EPG5). The prevalence of Vici syndrome is reported to be less than 1/1,000,000. Fetal ultrasonography detected right ventricular hypertrophy and hypoplastic left ventricle. After birth, hypopigmentation, agenesis of the corpus callosum, cerebellar hypoplasia, and progressive dysphagia were confirmed. Right ventricular hypertrophy was ameliorated after delivery. In addition, analysis of the T-cell receptor repertoire revealed that the expansion of Vβ2 and the absence of Vβ7.2 were observed in the peripheral T-cell populations. Genetic analysis detected two novel compound heterozygous mutations with pathogenicity: NM_020964.2: c.1779del (p.Phe594Leufs*17), c.5734_5741dup (p.Phe1914Leufs*17), and a variant of uncertain significance: c.7166T>C (p.Leu2389Ser) in EPG5. Early detection of immunodeficiency enabled the administration of antibiotic prophylaxis and subcutaneous immunoglobulin replacement before recurrent infection. Generally, Vici syndrome has a dismal prognosis; however, early supportive measures, including immunoprophylaxis and total gastric tube feeding might contribute to favorable outcomes.
In this study, we aimed to identify the gene abnormality responsible for pathogenicity in an individual with an undiagnosed neurodevelopmental disorder with megalencephaly, ventriculomegaly, hypoplastic corpus callosum, intellectual disability, polydactyly and neuroblastoma. We then explored the underlying molecular mechanism.Trio-based, whole-exome sequencing was performed to identify disease-causing gene mutation. Biochemical and cell biological analyses were carried out to elucidate the pathophysiological significance of the identified gene mutation.We identified a heterozygous missense mutation (c.173C>T; p.Thr58Met) in the MYCN gene, at the Thr58 phosphorylation site essential for ubiquitination and subsequent MYCN degradation. The mutant MYCN (MYCN-T58M) was non-phosphorylatable at Thr58 and subsequently accumulated in cells and appeared to induce CCND1 and CCND2 expression in neuronal progenitor and stem cells in vitro. Overexpression of Mycn mimicking the p.Thr58Met mutation also promoted neuronal cell proliferation, and affected neuronal cell migration during corticogenesis in mouse embryos.We identified a de novo c.173C>T mutation in MYCN which leads to stabilisation and accumulation of the MYCN protein, leading to prolonged CCND1 and CCND2 expression. This may promote neurogenesis in the developing cerebral cortex, leading to megalencephaly. While loss-of-function mutations in MYCN are known to cause Feingold syndrome, this is the first report of a germline gain-of-function mutation in MYCN identified in a patient with a novel megalencephaly syndrome similar to, but distinct from, CCND2-related megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome. The data obtained here provide new insight into the critical role of MYCN in brain development, as well as the consequences of MYCN defects.
Chromosome 1p32-p31 deletion syndrome involving the Nuclear factor I/A (NFIA) gene is characterized by corpus callosum hypoplasia or defects and urinary tract defects. Herein we report on a case resembling the 1p32-p31 deletion syndrome carrying a de novo truncating mutation (c.1094delC; p.Pro365Hisfs*32) in the NFIA gene, confirming that haploinsufficiency of the NFIA gene is a major determinant of this syndrome.
