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. 2022 Sep 6;17:345. doi: 10.1186/s13023-022-02499-z

Table 1.

Summary of candidate variants identified and in silico prediction scores in the patient

Gene Protein ID DNA change AA change gnomAD TOPMED GERP CADD REVEL
CACNA1I Q9P0X4 82C>T P28S n.d 8.00E−06 1.27 14.69 0.350
1747G>A A583T 2.42E−03 3.76E−03 −0.55 0.67 0.244
NIN Q8N4C6 5264C>T A1755V 2.10E−05 1.10E−05 4.50 19.36 0.078
6348A>G I2116M 2.10E−05 1.10E−05 1.79 13.81 0.218
KCNH5 Q8NCM2 2566A>C N856H n.d n.d 5.92 21.50 0.531

gnomAD and TOPMED databases gather previously reported variation frequencies. GERP tool display a conservation score for a nucleotide position, values above 3 are considered as highly conserved. CADD tool scores the predicted deleteriousness of a variant (SNP or indels), values above 20 can be considered as “likely deleterious”. REVEL method combines 13 individual tools to predict the pathogenicity of missense variants, with scores from 0 to 1, it is estimated “likely disease causing” when above 0.5