BG05 Artificial intelligence prediction of splice site mutation consequences in junctional epidermolysis bullosa: signposts to severity

Abstract Over one-fifth of disease-causing mutations in junctional epidermolysis bullosa (JEB) are splice site variants. These affect pre-mRNA splicing through the activation cryptic sites and/or exon skipping, resulting altered mRNA and translated proteins. Prediction precise location activated is vital, as these can potentially alter reading frame transcript. Out-of-frame transcripts contain premature termination complexes (PTCs), which generally result nonfunctional protein often correlate with severe JEB conjunction other PTC-introducing mutations. SpliceAI a 32-layer convolutional neural network that examines 10 000 nucleotides flanking sequence around variant interest to predict its effects on RNA splicing. It was used mutation consequences five patients LAMB3 Genotypes, predicted subtypes summarized Table 1. PTCs cases 1 2, where were either out or novel introduced following aberrant An in-frame transcript no PTC for case 3, may explain this individual’s mild phenotype. Reverse transcriptase polymerase chain reaction data reviewed 4 5, two confirmed. Two additional not by found be produced low levels. likely generated partially functional protein, alleviating severity degree. This study highlights importance examining accurate genotype–phenotype correlation. In silico tools such show potential elucidating mechanisms severity. They facilitate selection further laboratory investigation guide regions gene confirmatory analyses. Where analyses available, correctly resultant transcripts. Further validation tool required rare disease.Table 1Genotypes, SpliceAICaseZygosityMutation (LAMB3)Exon skipping predictionCryptic predictionPredicted outcome commentsJEB subtype1Homozygousc.2701+1G>AOOF 18 skipping20 nt excluded from 18Both outcomes OOFSevere2Heterozygousc.565-2A>G, c.2914C>T (p.R972X)OOF 7 skipping117 included intron 6 (including TGA at c.565-60)In-frame introducedSevereOOF skipping3Heterozygousc.1705C>T (p.R569X), c.943+2T>COOF 9 skipping27 9In-frame activationIntermediateOOF skipping4Homozygousc.298+5G>COOF skipping64 4Both OOFIntermediate5Heterozygousc.3119G>A (p.W1040X), c.629-12T>APredicted unlikely10 7OOF activationIntermediatent, nucleotides; OOF, frame.