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Table 2 RNA pathogenicity predictions in MToolBox with corresponding scores

From: A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs

rRNA prediction

rRNA Score

RNA pathogenicity score in MToolBox

tRNA Score

tRNA prediction

Proven pathogenic

5

1.000

20

Definitely pathogenic

0.950

19

Definitely pathogenic

0.900

18

Definitely pathogenic

0.850

17

Definitely pathogenic

Expectedly pathogenic

4

0.800

16

Definitely pathogenic

0.750

15

Definitely pathogenic

0.700

14

Definitely pathogenic

0.650

13

Possibly/definitely pathogenic

Likely pathogenic

3

0.600

12

Possibly/definitely pathogenic

0.550

11

Possibly/definitely pathogenic

0.500

10

Possibly pathogenic

0.450

9

Possibly pathogenic

Not enough evidence

2

0.400

8

Possibly pathogenic

0.350

7

Possibly pathogenic

0.300

6

Neutral

0.250

5

Neutral

Undetermined

1

0.200

4

Neutral

0.150

3

Neutral

0.100

2

Neutral

0.050

1

Neutral

Unlikely pathogenic

0

0.000

0

Neutral

  1. RNA pathogenicity scores provided by MToolBox pipeline, shown in the central column of the table, derived from two different scoring systems for rRNA and tRNA genes, respectively. Original predictions and scores, reported on the right and the left of MToolBox scores, were retrieved from the literature and normalized to a 0–1 range. Thresholds of 0.600 for rRNA and 0.350 for tRNA sequence variations (in bold) were set according to original scores. Damaging effects could be observed for variants with a score above or equal to the chosen thresholds, while neutral variants should be associated with lower values