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Table 3 Analysis of variants by bibliography and in silico predictive tools

From: Genotype–phenotype correlation of 17 cases of Pompe disease in Spanish patients and identification of 4 novel GAA variants

Nucleotide change Effect on protein ClinVar Mutation taster PolyPhen-2 VarSome HGMD Pompe database
Described mutations
c.-32-13T>G Pathogenic Pathogenic 33 Potentially mild
c.236_246del p.Pro79fsArgfs*13 Pathogenic Disease causing Pathogenic 34 Very severe
c.281_282delCT Pro94ArgfsTer51 Likely pathogenic Disease causing Pathogenic
c.655G>A p.Gly219Arg Pathogenic Disease causing Probably damaging Pathogenic 35 Potentially less severe
c.854C>G p.Pro285Arg Pathogenic Disease causing Probably damaging Likey pathogenic 36 Potentially mild
c.875A>G p.Tyr292Cys Pathogenic Disease causing Probably damaging Pathogenic 37 Potentially mild
c.925G>A p.Gly309Arg Pathogenic Disease causing Probably damaging Pathogenic 38 Potentially less severe
c.1396_1397insG p.Val466fs*39 Not described Disease causing Pathogenic
c.1655T>C p.Leu552Pro Pathogenic Disease causing Probably damaging Pathogenic 39 Potentially less severe
c.2065G>A p.Glu689Lys Conflicts of interpretation Polymorphism Likely bening Benign 40
c.2104C>T p.Arg702Cys Pathogenic Disease causing Probably damaging Pathogenic 41, 42 Potentially less severe
c.2237G>C p.Trp746Ser Not described Disease causing Probably damaging Pathogenic 43 Potentially less severe
Novel mutations
c.1328A>T p.Asp443Val Not described Disease causing Probably damaging Likely pathogenic
c.1831G>A p.Gly611Ser Not described Disease causing Probably damaging Pathogenic
c.1889-1G>A Not described Disease causing Pathogenic
c.2819C>A p.Ser940Ter Not described Disease causing Likely Pathogenic