Molecular study of Pompe disease in Egyptian infants

Egyptian Journal of Medical Human Genetics

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

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
AGVGD^e	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)
Blosum62^h	− 3	1

^aMutationTaster score ranges from 0.0 (polymorphism) to 215 (disease causing)
^bVariants with score ≤ − 2.5 are “damaging” and variants with score ˃ − 2.5 are “neutral”
^cVariants with score ≤ 0.05 are "deleterious” and variants with score ˃ 0.05 are “tolerated”
^dPolyPhen2 score ranges from 0 (tolerated) to 1 (deleterious)
^eAGVGD classes: C0 (least likely to interfere with function), C15, C25, C35, C45, C55, C65 (most likely to interfere with function)
^fThe SNPs&GO reliability index extends from 1 (neutral) to 10 (disease-related)
^gMUTPRED predictions are considered “deleterious” if the score is > 0.5
^hIn Blosum62 matrix, a positive score implies that substitution is more likely than any random substitution and vice versa