Table 2.
List of five variants identified and eight strong candidate variants.
| rsID | Variant Name | Ref | Alt | CLNSIG | Power | OR | L95 | U95 | Penetrance | PL95 | PU95 | MAF (MAC) cases | MAF (MAC) controls | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| R1 | rs34637584 | LRRK2 p.G2019S | G | A | P/R | 0.97 | 11.8 | 10.5 | 13.2 | 0.3 | 0.2 | 0.3 | 0.01 (470) | 0.001 (3,385) |
| rs76763715 | GBA1 p.N409S | T | C | P/R | 1.00 | 2.3 | 2.0 | 2.5 | 0.0 | 0.0 | 0.1 | 0.01 (487) | 0.006 (18,190) | |
| rs75548401 | GBA1 p.T408M | G | A | C/U/U | 1.00 | 1.5 | 1.4 | 1.6 | 0.0 | 0.0 | 0.0 | 0.02 (206) | 0.009 (1,013) | |
| rs2230288 | GBA1 p.E365K | C | T | C/U/U | 1.00 | 1.4 | 1.3 | 1.5 | 0.0 | 0.0 | 0.0 | 0.03 (1,099) | 0.02 (74,759) | |
| rs34424986 | PRKN p.R275W | G | A | P | 1.00 | 1.3 | 1.1 | 1.5 | NA | NA | NA | 0.004 (138) | 0.003 (8,532) | |
| R2.1 | rs34995376 | LRRK2 p.R1441H | G | A | P | 0.06 | 43.0 | 13.8 | 133.9 | 0.8 | 0.2 | 1.0 | 2e-04 (6) | 0 (14) |
| rs80356771 | GBA1 p.R502C | G | A | P | 0.60 | 3.8 | 2.7 | 5.4 | 0.1 | 0.0 | 0.1 | 0.001 (45) | 4e-04 (1,271) | |
| rs78973108 | GBA1 p.R296Q | C | T | P | 0.10 | 3.7 | 2.1 | 6.5 | 0.9 | 0.2 | 1.0 | 1e-04 (4) | 0 (10) | |
| rs147138516 | GBA1 p.D179H | C | G | C/U/U | 0.41 | 3.3 | 2.1 | 5.0 | 0.0 | 0.0 | 0.1 | 2e-04 (6) | 1e-04 (272) | |
| rs111910483 | LRRK2 p.L1795F | G | T | C/U/U | 0.30 | 2.5 | 1.6 | 3.8 | 0.1 | 0.0 | 0.4 | 4e-04 (2) | 1e-04 (53) | |
| R2.2 | rs28365216 | LRRK2 p.N238I | A | T | C/U/U | 0.05 | 9.4 | 1.5 | 58.1 | 0.6 | 0.1 | 1 | 1e-04 (2) | 0 (3) |
| rs80356769 | GBA1 p.V433L | C | A | P | 0.13 | 4.18 | 1.99 | 8.77 | 0.11 | 0.05 | 0.2 | 3e-04 (9) | 0 (149) | |
| rs201106962 | SNCA p.H50Q | A | C | C/U/U | 0.64 | 2.0 | 1.2 | 3.5 | 0.05 | 0.02 | 0.1 | 0.001 (10) | 4e-04 (18) |
R1 are variants in our main results, having passed 80% and Bonferroni correction. R2 describes variants not passing 80% power with ORs greater than 2. R2.1 are variants passing Bonferroni correction, R2.2 are pathological variants passing p value < 0.05, dominantly inherited genes, and previously linked to PD. Variants in the R2 group are strong candidates for a potential association with PD, based on their high ORs and p value status. More information can be found in Supplementary Table 8. Variants with wide confidence intervals should be interpreted carefully.
Ref reference allele, Alt alternate allele, CLNSIG clinical significance based on ClinVar, Power statistical power at OR = 2 and alpha=0.05, OR odds ratio, L95 Lower boundary 95% confidence interval, U95 upper boundary 95% confidence interval, PL95 Lower boundary 95% confidence interval penetrance, PU95 Upper boundary 95% confidence interval penetrance, MAF minor allele frequency, MAC minor allele count, P pathogenic, P/R pathogenic/risk factor, C/U/U conflicting, uncertain, unknown.