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Table 2 In silico prediction of pathogenic effect of MLL2 missense and splice site variants

From: Mutation spectrum of MLL2 in a cohort of kabuki syndrome patients

     Prediction of damaging effect at the protein level   
ID Exon Mutation AA change    MutPred Rescue-ESE Fas-ESS
     Polyphen Align GVGD Probability of deleterious mutation Confident in silico hypothesis   
KB32 11 c.3773G>A p.Arg1258Gln benign deleterious 0.16 loss of loop (p = 0.0288, loss of catalytic residue at R1258 (p = 0.0301); gain of helix (p = 0.0349) no change no change
KB28 15 c.[4249A>G;4252C>A] p.[Met1471Val;Leu1418Met] benign; benign deleterious; deleterious 0.46; 0.47 none; none no change gain of one ESS
KB34 16 c.4565A>G p.Gln1522Arg benign deleterious 0.50 none loss of one ESE no change
KB27 34 c.8521C>A p.Pro2841Thr possibly damaging deleterious 0,24 gain of phoshorylation P2841 (p = 0.028) gain of two ESEs loss of one ESS
KB38 48 c.[15084C>G;15100T>G] p.[Asp 5028Glu;Phe5034Val] benign; benign deleterious; deleterious 0.42; 0.56 none; none gain of three ESEs loss of three ESSs
KB76 48 c.1517A>C p.His5059pro benign deleterious 0,71 none no change no change
KB17 50 c.16019G>A p.Arg5340Gln benign deleterious 0,53 gain of ubiquitination at K5344 (p = 0.0396) gain of two ESEs no change
ID Intron Mutation Splice site modification prediction Predicted Protein Conclusion
     NetGene NNSplice     
KB31 Intron 3-4 c.400+1G>A Loss of DS Loss of DS 135 AA with novel 2 AA deleterious
KB20 Intron 3-4 c.401-3A>G New AS at-3 New AS at-3 217 AA with novel 84 AA deleterious
KB29 Intron 42-43 c. 13999+5 G>A Lower confidence of DS prediction Lower confidence of DS prediction   unpredictable