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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