Table 3. In silico analyses of two novel variants.
| SNPs | Sequence alterationa | PolyPhen-2 (SCOREb) | SIFT (SCOREc) | PROVEAN (SCOREd) | Mutation taster (P-valuee) | Mutation assessor (SCOREf) |
|---|---|---|---|---|---|---|
| Novo 1 | c.460C>G:p.(R154G) | Probably damaging (1.000) | Damaging (0.015) | Deleterious (−4.60) | Disease causing (0.999) | Medium (2.935) |
| Novo 2 | c.584G>T:p.(R195M) | Probably damaging (1.000) | Damaging (0.000) | Deleterious (−4.76) | Disease causing (0.999) | Medium (3.185) |
a
The reference sequence was human reference genome (GRCh37/hg19) from the National Center for Biotechnology Information.
b
Scores range from 0 to 1, with high scores being assigned to damaging variants.
c
Cutoff=0.05. Amino acid substitutions are predicted to be damaging if ≤0.05 and tolerated if >0.05.
d
Cutoff=−2.5. Amino acid substitutions are predicted to be damaging if ≤−2.5 and tolerated if >2.5.
e
Values close to 1 indicate a high predictive value. The P-value is not the probability of error as used in t-test statistics.
f
Cutoff=1.938. Amino acid substitutions are predicted to be non-functional (neutral to low) if ≤1.938 and functional (medium to high) if >1.938.