Characterising the loss-of-function impact of 5’ untranslated region variants in whole genome sequence data from 15,708 individuals

Abstract

Upstream open reading frames (uORFs) are important tissue-specific cis -regulators of protein translation. Although isolated case reports have shown that variants that create or disrupt uORFs can cause disease, genetic sequencing approaches typically focus on protein-coding regions and ignore these variants. Here, we describe a systematic genome-wide study of variants that create and disrupt human uORFs, and explore their role in human disease using 15,708 whole genome sequences collected by the Genome Aggregation Database (gnomAD) project. We show that 14,897 variants that create new start codons upstream of the canonical coding sequence (CDS), and 2,406 variants disrupting the stop site of existing uORFs, are under strong negative selection. Furthermore, variants creating uORFs that overlap the CDS show signals of selection equivalent to coding loss-of-function variants, and uORF-perturbing variants are under strong selection when arising upstream of known disease genes and genes intolerant to loss-of-function variants. Finally, we identify specific genes where perturbation of uORFs is likely to represent an important disease mechanism, and report a novel uORF frameshift variant upstream of NF2 in families with neurofibromatosis. Our results highlight uORF-perturbing variants as an important and under-recognised functional class that can contribute to penetrant human disease, and demonstrate the power of large-scale population sequencing data to study the deleteriousness of specific classes of non-coding variants.

uORFlight: a vehicle towards uORF-mediated translational regulation mechanisms in eukaryotes

“…uORF variation has been studied at the genome-wide scale using human SNPs and the results provide clear evidence of its association with genetic diseases. However, these studies only assessed single SNP effects that result in uORF initiation codon creation or stop codon loss (3, 8). We analyzed uORF variation by considering the integral effect of all homozygous SNPs and INDELs in each accession.…”

“…By 2009, 509 human genes had been identified with polymorphic uORFs and some of them have been experimentally associated with different human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. This trend became more striking recently with more genomic variation data released and analyzed (3, 8). In contrast, natural variation of plant uORFs has not yet been investigated, even though there are abundant publicly accessible genetic and phenotypic variation data, especially for Arabidopsis ( Arabidopsis thaliana ) and rice ( Oryza sativa L.).…”

Annotating high-impact 5’untranslated region variants with the UTRannotator

“…Upstream open reading frames (uORFs) are short sequences within 5'UTRs that regulate the rate at which the downstream coding sequence is translated into protein. Variants that create or disrupt uORFs (uORF-perturbing variants) have been shown to cause rare disease (Calvo, Pagliarini and Mootha, 2009;Whiffin et al, 2020). We recently used data from the Genome Aggregation Database (gnomAD) to systematically characterise the deleteriousness of different categories of uORF-perturbing variants and prioritise those that are more likely to be disease causing (Whiffin et al, 2020).…”

“…Variants that create or disrupt uORFs (uORF-perturbing variants) have been shown to cause rare disease (Calvo, Pagliarini and Mootha, 2009;Whiffin et al, 2020). We recently used data from the Genome Aggregation Database (gnomAD) to systematically characterise the deleteriousness of different categories of uORF-perturbing variants and prioritise those that are more likely to be disease causing (Whiffin et al, 2020). Current variant annotation approaches focus on the impact of protein-coding variants, with only limited annotation of predicted consequences for non-coding variants.…”

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

“…In other work, AS was shown to regulate domains leading to the rewiring of PPI networks in cancer 32 . Similarly, APA has been postulated as a mechanism to escape microRNA regulation by shortening 3' UTR regions 33,34 , alternative TSS are believed to regulate the inclusion of Upstream Open Reading Frames (uORFs) that control translational rates [35][36][37] and NMD has been proposed to regulate gene expression in cancer and neural systems 38,39 .…”