Using exome-sequencing for the diagnosis of rare disorders: two siblings affected by a congenital encephalopathy with microcephalia, polimicrogyria and dystonia

Exome sequencing was performed on two siblings of a Sardinian family affected by a severe, congenital encephalopathy characterized by microcephalia, polymicrogyria and dystonia. MPS was achieved with the platform HiSeq2000 (Illumina). Quality filtered reads were aligned to the human reference hg19. SNPs and in/dels were detected using Samtools and BWA softwares. To obtain a list of candidate genes, the variants were filtered against a set of polymorphisms available in public databases (dbSNP138, 1000Genomes, ESP6500) and prioritized with Ingenuity Variant Analysis software. This analysis led us to identify in both siblings an homozygous variant in a gene of the MBT (Malignant Brain Tumor) family, expressed in mammalian brain. This variation causes a Ser-Asn substitution in one of the MBT domains. The MBT domain is a “chromatin reader”, a protein module that recognizes mono/di-methylated lysines on histones tails. The MBT proteins interact with the enzymes that catalyze the histones methylation. This interaction plays a role in the repression of target genes. Although the pathway of the candidate gene is not well characterized, several studies show that its ortholog downregulates genes expressed in the early stages of neuronal development in Drosophila. In a preliminary study in vitro we have found that the protein binds the dimethyltransferases SUV4-20H demonstrating its involvement in the process of histone methylation. We speculate that the variant protein in our patients could destabilize the interaction between the MBT domain and the dimethyltransferases, altering the affinity for methylated histones and presumably its repressive properties.