uORF-creating mutations in Van der Woude syndrome: why it is important to study 5’UTRs

Abstract

International audienceBackground/Objectives:Van der Woude syndrome (VWS, MIM 119300) is an autosomal dominant cleft lip and/or palate with typical lower lip pits. Most patients carry loss-of-function mutations in IRF6. Upstream open reading frame (uORF)-creating mutations have been reported in four VWS patients. Pathogenic uORFcreating mutations are mostly out-of-frame upstream start codons (uAUG) in the 5’UTR. We searched for IRF6 uORF mutations and assessed the ability to predict the pathogenicity of uORFcreating variations of 5 prediction tools.Methods:We analyzed IRF6 UTR and coding regions in 68 VWS probands. By using a set of 44 reference genes, we assessed 5 in silico tools predicting the probability of ATGs to initiate translation: NetStart, ATGpr, TIS Miner, AltORFev, TIS Predictor. We then assessed the potential pathogenicity of all the theoretical uORFs in IRF6 5’UTR.Results:We have identified two novel uORF-creating mutations (c.-141C>T and c.-162C>T), representing 3% (2/68) of the probands. The 7 carriers of the two families had typical VWS signs. Our in silico analyses revealed a higher accuracy for AI-based tools over those based on Kozak consensus scoring. There are 28 theoretical uAUG-creating SNVs in IRF6 5’UTR. With AI-based tools, the six uAUG identified in VWS patients have high translation initiation site scores; 3 to 4 of the theoretical uAUG-creating SNVs had high scores and could correspond to pathogenic mutations. For the dozen of theoretical SNVs with intermediate scores, predicting pathogenicity remains challenging.Conclusion:As untranslated regions are frequently understudied in NGS strategies, uORF-creating mutations may be underdiagnosed in VWS and in human pathology in general