Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement

Abstract

BackgroundWhole-exome sequencing has identified the causes of several Mendelian diseases by analyzing multiple unrelated cases, but it is more challenging to resolve the cause of extremely rare and suspected Mendelian diseases from individual families. We identified a family quartet with two children, both affected with a previously unreported disease, characterized by progressive muscular weakness and cardiomyopathy, with normal intelligence. During the course of the study, we identified one additional unrelated patient with a comparable phenotype.MethodsWe performed whole-genome sequencing (Complete Genomics platform), whole-exome sequencing (Agilent SureSelect exon capture and Illumina Genome Analyzer II platform), SNP genotyping (Illumina HumanHap550 SNP array) and Sanger sequencing on blood samples, as well as RNA-Seq (Illumina HiSeq platform) on transformed lymphoblastoid cell lines.ResultsFrom whole-genome sequence data, we identified RBCK1, a gene encoding an E3 ubiquitin-protein ligase, as the most likely candidate gene, with two protein-truncating mutations in probands in the first family. However, exome data failed to nominate RBCK1 as a candidate gene, due to poor regional coverage. Sanger sequencing identified a private homozygous splice variant in RBCK1 in the proband in the second family, yet SNP genotyping revealed a 1.2Mb copy-neutral region of homozygosity covering RBCK1. RNA-Seq confirmed aberrant splicing of RBCK1 transcripts, resulting in truncated protein products.ConclusionsWhile the exact mechanism by which these mutations cause disease is unknown, our study represents an example of how the combined use of whole-genome DNA and RNA sequencing can identify a disease-predisposing gene for a novel and extremely rare Mendelian disease.

Differential Involvement of the Npl4 Zinc Finger Domains of SHARPIN and HOIL-1L in Linear Ubiquitin Chain Assembly Complex-Mediated Cell Death Protection

“…Given that HOIP levels were lower in interferon-treated cpdm keratinocytes than in WT keratinocytes, augmented activation of antiapoptotic NF-B mediated by an increase in HOIL-1L/HOIP-containing LUBAC might not be able to completely override the augmented cell death caused by loss of SHARPIN. Some humans lacking HOIL-1L, however, exhibit autoinflammation and immunodeficiency in addition to amylopectinosis in early childhood (30), whereas in other cases, mutations in the HOIL-1L gene cause various degrees of myopathies without immunological symptoms beginning in childhood or the juvenile years (39,41). We have not observed any overt inflammatory diseases in HOIL-1L KO or HOIL-1L Ϫ/Ϫ SHARPIN ϩ/cpdm mice, at least by 12 weeks of age ( Fig.…”

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“…Homozygous or compound heterozygous RBCK1 mutations are associated with early onset of disease, which includes polyglucosan accumulation in several tissues, skeletal myopathy, and rapidly progressing cardiomyopathy (Boisson et al, 2012;Nilsson et al, 2013;Wang et al, 2013). Two distinct phenotypes have been described.…”

Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome

“…While our study identified an unexpected noncoding mutation in a novel disease gene, several prior studies have also shown the potential of RNA-seq for discovering splicing perturbations in known human disease genes (Chandrasekharappa et al 2013), splicing defects caused by variants in canonical (i.e., predictable) splice sites of genes not previously associated with disease (Wang et al 2013), fusion transcripts in cancer (Pierron et al 2012;Morin et al 2013), and RNA-seq confirmation of known transcription-altering mutations from genetic screens in model organisms (Miller et al 2013). These studies also identified decreased transcript levels due to nonsense-mediated decay and other unexpected splice defects such as missense and synonymous exonic mutations causing exon skipping (Chandrasekharappa et al 2013;Miller et al 2013).…”