A homozygous synonymous NOP58 variant causes a neurodevelopmental disorder by impairing maturation of pre-ribosomal RNAs.

Ribosomes are ribonucleoproteins that are responsible for protein synthesis. They consist of ribosomal proteins and ribosomal RNAs (rRNAs). Pre-rRNAs are co-transcriptionally processed and chemically modified. The 2'-O-methylation of rRNAs is guided by box C/D small nucleolar ribonucleoprotein particles (snoRNPs), which are composed of a box C/D snoRNA and the core proteins NOP56, NOP58, SNU13, and the methyltransferase fibrillarin. Catalytically active box C/D snoRNPs function in nucleoli. We performed trio whole-exome sequencing in a proband with a severe neurodevelopmental disorder including global developmental delay, microcephaly, seizures, and ophthalmological and brain abnormalities and his healthy parents and identified the homozygous synonymous variant c.516G>A; p.Leu172= in NOP58. In fibroblasts of the proband, we demonstrated skipping of exon 7 in most NOP58 mRNAs, while ∼20% canonically spliced NOP58 transcripts were detected in the proband compared with control cells. NOP58 protein levels were reduced to ∼12% in proband cells that concomitantly reduced fibrillarin levels. Analysis of nucleoli in proband-derived fibroblasts revealed changes in the number of nucleolar condensates and in nucleolar morphology. We found reduced levels of three box C/D snoRNAs required for 2'-O-methylation and of one box C/D snoRNA important for 2'-O-methylation and pre-rRNA processing. Analysis of pre-rRNA maturation by RT-qPCR revealed increased 45S and 21S pre-rRNA levels, whereas the amplification signal for the 47S, 32S, and 26S pre-rRNAs was substantially decreased in proband compared with control cells. Together, our data unveil that the homozygous NOP58 variant c.516G>A represents a hypomorphic allele and underlies the neurodevelopmental phenotype in the proband, likely by impairing pre-rRNA maturation.