Without exception, a highly significant difference was observed using every deleteriousness metric with M-CAP the most significant ( p = 1.37 × 10 − 4 ) all of which would withstand correction for the three independent tests performed.
In a Parkinson’s Disease (PD) cohort of very modest sample size compared to contemporary GWAS studies, GenePy successfully identified association with the PINK1 gene but failed to reach significance for five other known genes when looking across the entire distribution of scores.
Only modestly significant differences for just three of the implemented deleteriousness metrics (M-CAP, fathmm-mkl and MutTaster) were observed comparing all IBD against controls in this relatively small sample.