Table 2.
T2D-ESKD associated variants in meta-analysis from discovery and replication cohorts (baseline model)
| Variant | Gene | Annotation | CHR | POS | EA | Discovery (456 T2D-ESKD cases vs. 936 nondiabetic non-nephropathy controls) |
Replication (2020 T2D-ESKD cases vs. 1121 nondiabetic non-nephropathy controls) |
Meta-analysis (2476 T2D-ESKD cases vs. 2057 nondiabetic non-nephropathy controls) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EAF | OR (95% CI) | P | EAF | OR (95% CI) | P | Info | EAF | OR (95% CI) | P | Q-value | ||||||
| rs59928984 | PLEKHN1 | Intron | 1 | 907622 | C | 0.22 | 1.46 (1.15–1.85) | 0.0017 | 0.21 | 1.27 (1.08–1.50) | 0.0041 | 0.91 | 0.21 | 1.33 (1.16–1.53) | 3.32E-05 | 0.023 |
| rs180881514 | NADK | Intron | 1 | 1685713 | T | 0.01 | 4.87 (1.96–12.06) | 0.00064 | 0.011 | 2.23 (1.20–4.13) | 0.011 | 0.91 | 0.011 | 2.85 (1.71–4.75) | 5.84E-05 | 0.031 |
| rs834514 | RAD51AP2 | Missense | 2 | 17696573 | T | 0.21 | 0.7 (0.55–0.89) | 0.0037 | 0.21 | 0.79 (0.68–0.93) | 0.0043 | 1.0 | 0.21 | 0.76 (0.67–0.87) | 6.56E-05 | 0.032 |
| rs665312 | RAD51AP2 | Synonymous | 2 | 17698678 | G | 0.24 | 0.69 (0.55–0.86) | 0.0011 | 0.24 | 0.81 (0.70–0.95) | 0.0077 | 1.0 | 0.24 | 0.77 (0.68–0.87) | 5.27E-05 | 0.031 |
| rs41302867 | RREB1 | Intron | 6 | 7240876 | A | 0.023 | 0.35 (0.18–0.67) | 0.0016 | 0.02 | 0.51 (0.33–0.80) | 0.003 | 1.0 | 0.021 | 0.45 (0.31–0.65) | 2.43E-05 | 0.019 |
| rs9986447 | PEX6 | Splice region | 6 | 42942779 | G | 0.22 | 0.71 (0.56–0.89) | 0.0028 | 0.21 | 0.8 (0.68–0.94) | 0.0074 | 0.98 | 0.21 | 0.77 (0.67–0.88) | 9.04E-05 | 0.039 |
| rs74678433 | GRM8 | Intron | 7 | 126173950 | G | 0.026 | 2.73 (1.54–4.84) | 0.0006 | 0.028 | 1.92 (1.27–2.91) | 0.0019 | 0.95 | 0.027 | 2.17 (1.55–3.03) | 5.96E-06 | 0.014 |
| rs268672 | PRX | Synonymous | 19 | 40901604 | A | 0.19 | 0.73 (0.58–0.93) | 0.0096 | 0.2 | 0.77 (0.66–0.91) | 0.002 | 1.0 | 0.19 | 0.76 (0.66–0.87) | 5.87E-05 | 0.031 |
| rs268671 | PRX | Missense | 19 | 40901614 | A | 0.19 | 0.73 (0.58–0.93) | 0.0096 | 0.2 | 0.76 (0.64–0.89) | 0.00072 | 1.0 | 0.19 | 0.75 (0.65–0.86) | 2.11E-05 | 0.018 |
| rs73885319 | APOL1 | Missense | 22 | 36661906 | G | 0.23 | 1.39 (1.11–1.73) | 0.0036 | 0.24 | 1.29 (1.11–1.50) | 0.00076 | 1.0 | 0.24 | 1.32 (1.17–1.50) | 9.90E-06 | 0.014 |
| rs60910145 | APOL1 | Missense | 22 | 36662034 | G | 0.23 | 1.42 (1.14–1.77) | 0.0017 | 0.24 | 1.29 (1.11–1.50) | 0.00081 | 1.0 | 0.24 | 1.33 (1.18–1.51) | 5.74E-06 | 0.014 |
CHR, chromosome; CI, confidence interval; EA, effect allele; EAF, effect allele frequency; ESKD, end-stage kidney disease; Info, information metric reported by IMPUTE2; OR, odds ratio; POS, position; T2D, type 2 diabetes.
Baseline model: adjusted for age, sex. Annotation, derived from Variant Effect Predictor (VEP). APOL1 renal-risk genotype carriers included.