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Table 4 In silico analysis for the novel missense variant and the pseudodeficiency allele

From: Molecular study of Pompe disease in Egyptian infants

Tool c.1193 T > C (p.Leu398Pro) c.868A > G (p.Asn290Asp)
MutationTaster (score)a Disease causing (98) Disease causing (23)
PROVEAN (score)b Deleterious (− 3.108) Deleterious (− 4.525)
SIFT (score)c Damaging (0.019) Damaging (0.009)
PolyPhen2 (score)d probably damaging (0.998)
Sensitivity: 0.27
Specificity: 0.99
Probably damaging (1.000)
Sensitivity: 0.00 Specificity: 1.00
AGVGDe Class C65 Class C15
SNPs&GO (Reliability Index)f Disease-related (10) Disease-related (10)
MUTRED software (probability)g Deleterious (0.911) Deleterious (0.595)
Blosum62h  − 3 1
  1. aMutationTaster score ranges from 0.0 (polymorphism) to 215 (disease causing)
  2. bVariants with score ≤  − 2.5 are “damaging” and variants with score ˃ − 2.5 are “neutral”
  3. cVariants with score ≤ 0.05 are "deleterious” and variants with score ˃ 0.05 are “tolerated”
  4. dPolyPhen2 score ranges from 0 (tolerated) to 1 (deleterious)
  5. eAGVGD classes: C0 (least likely to interfere with function), C15, C25, C35, C45, C55, C65 (most likely to interfere with function)
  6. fThe SNPs&GO reliability index extends from 1 (neutral) to 10 (disease-related)
  7. gMUTPRED predictions are considered “deleterious” if the score is > 0.5
  8. hIn Blosum62 matrix, a positive score implies that substitution is more likely than any random substitution and vice versa