Table 1.
GBA variant frequencies in cases and controls
| Amino acid | GRCh38 (bp) | rs Number | Clinvar | HGMD pathogenicity | Cases |
Controls |
ExAC (EUR) |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| M/M | M/W | W/W | MAF | M/M | M/W | W/W | MAF | M/M | MAF | OR | P | |||||
| K13R (K-27R) | 155240707 | rs150466109 | Benign | DM? | 0 | 0 | 6249 | 0 | 0 | 2 | 6030 | 0.00017 | 0 | 0.00021 | NA | 0.999 |
| C62Y (C23Y) | 155240008 | rs145888253 | na | na | 0 | 1 | 6248 | 0.00008 | 0 | 0 | 6032 | 0 | 0 | 0.00001 | NA | 1 |
| E150K (E111K) | 155239622 | none | na | DM? | 0 | 1 | 6248 | 0.00008 | 0 | 0 | 6031 | 0 | 0 | 0 | NA | 0.9993 |
| F255Y (F216Y) | 155237576 | rs74500255 | Likely | Pathogenic | 0 | 2 | 6247 | 0.00016 | 0 | 1 | 6031 | 0.00008 | 0 | 0 | NA | 0.5827 |
| F298L (F259L) | 155237446 | none | na | pathogenic | 0 | 1 | 6248 | 0.00008 | 0 | 0 | 5990 | 0 | 0 | 0 | NA | 0.9993 |
| A348V (A309V) | 155236426 | rs78396650 | Pathogenic | Pathogenic | 0 | 5 | 6244 | 0.00040 | 0 | 0 | 6032 | 0 | 0 | 0 | NA | 0.9984 |
| E365K (E326K) | 155236376 | rs2230288 | Conflicting interpretations | DM? | 4 | 256 | 5989 | 0.02158 | 0 | 121 | 5911 | 0.01013 | 7 | 0.01196 | 2.037 | 1.64E-09 |
| T408M (T369M) | 155236246 | rs75548401 | Conflicting interpretations | DM? | 2 | 169 | 6078 | 0.01404 | 0 | 107 | 5925 | 0.00895 | 5 | 0.00976 | 1.53 | 0.001188 |
| N409S (N370S) | 155235843 | rs76763715 | Likely pathogenic | Pathogenic | 0 | 87 | 6161 | 0.00701 | 0 | 41 | 5991 | 0.00341 | 1 | 0.00363 | 1.882 | 0.002014 |
| D419N/Y | 155235814 | none | na | Pathogenic | 0 | 2 | 6247 | 0.00016 | 0 | 0 | 6032 | 0 | 0 | 0 | NA | 0.9991 |
| (D380N/Y) E427K (E388K) | 155235790 | rs149171124 | Uncertain significance | DM? | 0 | 10 | 6239 | 0.00080 | 0 | 5 | 6027 | 0.00041 | 0 | 0.00031 | NA | 0.2157 |
| na | 155390201 | rs71628662 | na | na | 1 | 187 | 6059 | 0.01513 | 0 | 88 | 5935 | 0.007305 | na | na | 2.07 | 1.324E-07 |
| na | 154925709 | rs114138760 | na | na | 1 | 166 | 6082 | 0.01344 | 0 | 107 | 5925 | 0.008869 | na | na | 1.52 | 0.0001853 |
Indicated are uncorrected P values (Bonferroni correction for 0.05 lies at > 0.0045) and odds ratios. Tests were carried out in plink using logistic regression with covariates age, sex, first 20 principal components based on genome-wide genotype data, and sample provenance.
Na, not applicable; bp, base pair; W, wild type; M, mutant; MAF, minor allele frequency; EUR, European; ExAC, Exorne Aggregation Consortium (http://exac.broadinstitute.org/); OR, odds ratio; HGMD, Human Gene Mutation Database.