EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type.
Pathogenic variants in the core spliceosome U5 small nuclear ribonucleoprotein gene EFTUD2/SNU114 cause the craniofacial disorder mandibulofacial dysostosis Guion-Almeida type (MFDGA). MFDGA-associated variants in EFTUD2 comprise large deletions encompassing EFTUD2, intragenic deletions and single nucleotide truncating or missense variants. These variants are predicted to result in haploinsufficiency by loss-of-function of the variant allele. While the contribution of deletions within EFTUD2 to allele loss-of-function are self-evident, the mechanisms by which missense variants are disease-causing have not been characterized functionally. Combining bioinformatics software prediction, yeast functional growth assays, and a minigene (MG) splicing assay, we have characterized how MFDGA missense variants result in EFTUD2 loss-of-function. Only four of 19 assessed missense variants cause EFTUD2 loss-of-function through altered protein function when modeled in yeast. Of the remaining 15 missense variants, five altered the normal splicing pattern of EFTUD2 pre-messenger RNA predominantly through exon skipping or cryptic splice site activation, leading to the introduction of a premature termination codon. Comparison of bioinformatic predictors for each missense variant revealed a disparity amongst different software packages and, in many cases, an inability to correctly predict changes in splicing subsequently determined by MG interrogation. This study highlights the need for laboratory-based validation of bioinformatic predictions for EFTUD2 missense variants.
['Thomas|Huw B|HB|0000-0001-9626-9706', 'Wood|Katherine A|KA|0000-0002-6459-2127', 'Buczek|Weronika A|WA|0000-0003-1131-8009', 'Gordon|Christopher T|CT|0000-0002-9300-8399', 'Pingault|Véronique|V|0000-0001-7064-0765', 'Attié-Bitach|Tania|T|0000-0002-1155-3626', 'Hentges|Kathryn E|KE|0000-0001-8917-3765', 'Varghese|Vinod C|VC|0000-0002-6512-6064', 'Amiel|Jeanne|J|0000-0001-5973-4728', 'Newman|William G|WG|0000-0002-6382-4678', "O'Keefe|Raymond T|RT|0000-0001-8764-1289"]
D019295:Computational Biology D005091:Exons D057895:Haploinsufficiency D006801:Humans D008607:Intellectual Disability D008342:Mandibulofacial Dysostosis D008831:Microcephaly D020125:Mutation, Missense D010445:Peptide Elongation Factors D012326:RNA Splicing D017415:Ribonucleoprotein, U5 Small Nuclear D017381:Spliceosomes
EFTUD2 missense variants mandibulofacial dysostosis Guion-Almeida type Snu114 yeast minigene pre-mRNA splicing splicing variants