Table 3 Evaluation of pathogenicity of novel variants using in-silico prediction tools
Gene | Mutation | Protein change | Mutation taster | LRT | SIFT | PROVEAN | DANN | ExAC | dbSNP |
|---|---|---|---|---|---|---|---|---|---|
ASS1 | c.190G > A | p.Val64Ile | Disease causing | Neutral | Tolerated | Neutral | 0.9791 | 0.00003303 | 556,297,791 |
c.269G > A | p.Gly90Asp | Disease causing | Unknown | Damaging | Damaging | 0.9985 | Not Present | 1,422,867,920 | |
c.271A > C | p.Thr91Pro | Disease causing | Unknown | Damaging | Damaging | 0.9963 | 0.00003324 | 769,018,733 | |
c.570C > A | p.Tyr190Ter | Disease causing | Unknown | NA | NA | 0.9957 | Not Present | Not Present | |
c.1139delA | p.Gln380Argfs*20 | Disease causing | NA | NA | NA | NA | Not Present | 1,213,378,896 | |
ASL | c.89_94delinsGTCGTA | p.Tyr30_Asp31delinsCysArg | Disease causing | NA | NA | NA | NA | Not present | Not present |
c.326C > G | p.Thr109Arg | Disease causing | Deleterious | Damaging | Damaging | 0.9938 | Not present | Not Present | |
c.593C > T | p.Pro198Leu | Disease causing | Deleterious | Damaging | Damaging | 0.9992 | Not Present | 1,282,829,485 | |
c.649C > T | p.Arg217Ter | Disease causing | Neutral | NA | NA | 0.9972 | 0.000008443 | 369,879,957 | |
c.733T > C | p.Trp245Arg | Disease causing | Deleterious | Damaging | Damaging | 0.9941 | Not present | Not Present | |
c.749T > A | p.Met250Lys | Disease causing | Deleterious | Damaging | Damaging | 0.9791 | Not present | 754,634,171 | |
c.913G > A | p.Gly305Arg | Disease causing | Deleterious | Damaging | Damaging | 0.9993 | Not present | Not Present | |
c.967A > G | p.Lys323Glu | Disease causing | Deleterious | Damaging | Damaging | 0.9987 | Not present | Not Present | |
OTC | c.773_790del | p.Asn258_263Del | Disease causing | NA | NA | NA | NA | Not present | Not Present |
c.805G > A | p.Gly269Arg | Disease causing | Deleterious | Damaging | Damaging | 0.9992 | Not Present | Not Present | |
ARG1 | c.2T > C | p.Met1Thr | Disease causing | Deleterious | Damaging | Neutral | 0.9809 | Not Present | Not Present |
c.132_146del | p.Gln44_Lys48del | Disease causing | NA | NA | NA | NA | Not Present | Not Present | |
c.295G > A | p.Gly99Arg | Disease causing | Deleterious | Damaging | Damaging | 0.9993 | 0.00001658 | 753,829,097 | |
c.551delC | p.Pro184Leufs*7 | Disease causing | NA | NA | NA | NA | Not Present | Not Present | |
c.802 + 2 T > G | Splice site | Disease causing | NA | NA | NA | 0.9948 | Not Present | Not Present | |
c.877delG | p.Val293Ter | Disease causing | NA | NA | NA | NA | Not Present | Not Present | |
CPS1 | c.254 + 4A > G | Splice site | Disease causing | NA | NA | NA | 0.9747 | Not Present | Not Present |
NAGS | c.787G > T | p.Glu263Ter | Disease causing | Deleterious | NA | NA | 0.9963 | Not Present | Not Present |
c.991C > T | p.Gln331Ter | Disease causing | Deleterious | NA | NA | 0.9973 | Not Present | 1,445,639,047 |