Skip to main content

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