Genetic Diagnosis of Charcot-Marie-Tooth Disease in a Population by Next-Generation Sequencing

Table 2

Classification of variants into five pathogenicity classes.

Pathogenicity class	Conclusion	Criteria
5	certainly pathogenic	(1) Reported pathogenic in at least two unrelated cases; (2) and/or functional studies reveal effect on protein structure/function; (3) and zygosity/inheritance of phenotype fits the variant; (4) and phenotype-genotype correlation with previously published literature
4	likely pathogenic	(1) Reported pathogenic in one case; (2) and/or predicted pathogenic in at least 2 of 4 variant prediction tools: SIFT [28], Polyphen [29], Align GVGD [30], and Mutation Taster [31] through the Alamut interface; (3) and/or predicted loss or gain of splice site predicted in at least 4 of 5 splice site predictors: SpliceSiteFinder [32], MaxEntScan [33], NNSPLICE [34], GeneSplicer [35], and Human Splicing Finder [36] through the Alamut interface; (4) and/or close proximity to known pathogenic mutations with similar or lower variant prediction score; (5) and zygosity/inheritance of phenotype fits the variant; (6) and phenotype-genotype correlation with previously published literature
3	uncertain pathogenic	(1) Present in ≤0.1% of dbSNP135 or 1000 genomes; (2) and/or present in ≤1 in-house control; (3) and zygosity/inheritance of phenotype in family fits the variant; (4) Variants in class 2 may be lifted to this class if present in several affected patients with similar phenotype
2	unlikely pathogenic	(1) Present in 0.1–1% of dbSNP135 or 1000 genomes; (2) and/or present in 2-3 in-house controls; (3) and/or predicted no loss or gain of splice site predicted by 5/5 splice site predictors (applies only to synonymous variants and variants in introns and UTRs); (4) and/or reported benign in the literature
1	certainly not pathogenic	(1) Present in ≥1% of dbSNP135 or 1000 genomes; (2) and/or present in ≥4 in-house controls

dbSNP = the single nucleotide polymorphism database.