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Table 1 Predicting the effect of detected variants

From: Variable predicted pathogenic mechanisms for novel MECP2 variants in RTT patients

Tool/database

C1076A (S359Y)

Ser359Tyr

TCC → TAC

C1207T (P403S)

Pro403Ser

CCT → TCT

G398A (R133H)

Arg133His

CGC → CAC

A362C (D121A)

Asp121Ala

GAT → GCT

MutationTaster2 (score)a

Disease causing (155)

Disease causing (74)

Disease causing (29)

Disease causing (126)

PROVEANb

Neutral (−1.189)

Neutral (−0.315)

Deleterious (−4.996)

Deleterious (−7.838)

PolyPhen2 (score)c

Benign (0.085)

Sensitivity: 0.93

Specificity: 0.85

Benign (0.141)

Sensitivity: 0.92

Specificity: 0.86

Probably damaging (1.000)

Sensitivity: 0.00 Specificity: 1.00

Probably damaging (1.000)

Sensitivity: 0.00 Specificity: 1.00

AGVGDd

Class C65

Class C65

Class C25

Class C65

SNPs&GO (reliability index)e

Neutral (8)

Neutral (9)

Disease-related (6)

Disease-related (5)

MutPred2 software (probability)f

Non-deleterious (0.197)

Non-deleterious (0.106)

Deleterious (0.721).

Deleterious (0.860)

Blosum62g

−2

−1

0

−2

ESEfinder 2.0h

Insignificant

Insignificant

Insignificant

Insignificant

  1. aMutationTaster score may range from 0.0 (polymorphism) to 215 (disease causing)
  2. bVariants with a score equal to or below −2.5 are considered “deleterious” and variants with a score above −2.5 are considered “neutral”
  3. cPolyPhen2 score ranges from 0.0 (tolerated) to 1.0 (deleterious)
  4. dAGVGD classes: C65 (most likely to interfere with function), C55, C45, C35,C25, 15, C0 (least likely to interfere with function)
  5. eThe SNPs&GO reliability index ranges from 1 to 10 (with 10 being the highest)
  6. fMUTPRED predictions are listed as “Deleterious” if the score is >0.5
  7. gIn the Blosum62 matrix, a positive score implies that substitution is more likely than any random substitution and vice versa
  8. hESEfinder adjusted to score the best hit in each sequence