TABLE 4.
In silico predictions of splice site alterations and pathogenicity of the detected variants in CKB, CKMT1B, and GATM. To analyze the putative effects of variants on splicing products, the tools ESEfinder (Cartegni et al., 2003) and Spliceman (Lim and Fairbrother, 2012) were applied. Predictions of pathogenicity and a conservation score were obtained by MutationTaster 2021 (Steinhaus et al., 2021). Non-synonymous variants are shown in bold.
| Gene | Variant | Amino acid exchange | ESEfinder | Spliceman | MutationTaster2021 | |
|---|---|---|---|---|---|---|
| Splice site changes | Splice site—rank (%) | Prediction | PhyloP score | |||
| CKB | rs762206402 | Pro112= | Changed | 55 | Neutral | −0.723 |
| rs1136165 | Arg152= | Changed | 70 | Neutral | −0.515 | |
| rs200890896 | Ala175= | Changed | 73 | Neutral | 0.247 | |
| rs146047573 | Tyr269Cys | Changed | 66 | Neutral | 2.167 | |
| rs1803283 | Glu364= | Changed | 60 | Neutral | 1.733 | |
| CKMT1B | g.43595061C/T | Thr79= | Changed | 58 | Neutral | 1.104 |
| g.43595385C/T | Asp120= | Not changed | 65 | Neutral | −0.388 | |
| g.43595451G/A | Thr142= | Changed | 77 | Neutral | −0.731 | |
| rs1230355611 | Arg184Stop | Changed | 63 | Deleterious | 2.353 | |
| rs758572075 | Val191Ala | Changed | 70 | Neutral | 1.217 | |
| rs9571 | Lys352= | Not changed | 64 | Neutral | 0.774 | |
| rs13234 | Ala362= | Changed | 71 | Neutral | 0.430 | |
| rs149544188 | Arg399= | Changed | 66 | Neutral | 2.638 | |
| rs144820945 | Gly403= | Changed | 57 | Neutral | −0.249 | |
| GATM | rs1288775 | Gln110His | Not changed | 47 | Neutral | 0.902 |
| rs146057680 | Asp234Val | Not changed | 63 | Deleterious | 4.283 | |
| rs773358289 | Pro287Ser | Changed | 68 | Deleterious | 4.949 | |
| rs747005297 | His292Arg | Changed | 58 | Deleterious | 4.099 | |
| rs1145086 | Leu481= | Changed | 64 | Neutral | 1.626 | |