Table 1 Results of gene burden testing for different gene masks of UQCRC1
Mask | Carrier | Case | BOLT-LMM | Logistic Regression | SKAT | ||||
|---|---|---|---|---|---|---|---|---|---|
Beta | SE | P | OR | P | PSKAT | PSKAT-O | |||
High confidence PTVa | 120 | 6 | 0.041 | 0.009 | 1.20E−06 | 6.59(2.84–15.27) | 1.12E-05 | 1.17E−06 | 4.34E−08 |
Missense variants with CADD > 0.25 | 990 | 6 | 0.003 | 0.009 | 3.20E−01 | 0.67(0.30–1.49) | 3.21E-01 | 9.44E−01 | 5.13E−01 |
Missense variants with AlphaMissense > 0.9 | 123 | 2 | 0.007 | 0.008 | 4.20E−01 | 1.82(0.45–7.43) | 4.04E-01 | 4.26E−01 | 5.92E−01 |
Missense variants with REVEL > 0.7 | 36 | 0 | – | – | – | – | – | – | – |
Missense variants with AlphaMissense > 0.7 | 241 | 3 | 0.003 | 0.006 | 6.20E−01 | 1.35(0.43–4.25) | 6.04E−01 | 5.08E−01 | 7.34E−01 |
Missense variants with AlphaMissense > 0.56 | 285 | 3 | 0.001 | 0.006 | 8.40E−01 | 1.15(0.37–3.60) | 8.12E−01 | 7.29E−01 | 9.14E−01 |
Missense variants with REVEL > 0.5 | 342 | 3 | 0.0004 | 0.005 | 9.20E−01 | 0.95(0.30–2.97) | 9.31E−01 | 6.13E−01 | 8.30E−01 |
Sensitivity Analyses | |||||||||
High confidence PTVa | 118 | 6 | 0.042 | 0.009 | 7.50E−07 | 6.79(2.92–15.77) | 8.37E−06 | 9.86E−07 | 1.42E−08 |
Missense variants with CADD > 0.25 | 976 | 6 | 0.003 | 0.008 | 3.40E−01 | 0.68(0.30–1.51) | 3.42E−01 | 9.43E−01 | 5.42E−01 |
Missense variants with AlphaMissense > 0.9 | 122 | 2 | 0.007 | 0.008 | 4.00E−01 | 1.88(0.46–7.68) | 3.79E−01 | 4.00E−01 | 5.59E−01 |
Missense variants with REVEL > 0.7 | 36 | 0 | – | – | – | – | – | – | |
Missense variants with AlphaMissense > 0.7 | 240 | 3 | 0.003 | 0.006 | 6.00E−01 | 1.38(0.44–4.33) | 5.82E−01 | 4.85E−01 | 7.10E−01 |
Missense variants with AlphaMissense > 0.56 | 283 | 3 | 0.001 | 0.006 | 8.20E−01 | 1.17(0.37–3.66) | 7.89E−01 | 7.06E−01 | 9.00E−01 |
Missense variants with REVEL > 0.5 | 340 | 3 | 0.0005 | 0.005 | 9.30E−01 | 0.96(0.31–3.00) | 9.43E−01 | 6.11E−01 | 8.29E−01 |
