Table 2 Top results of the genome-wide burden analysis for rare pLOF variants increasing the risk of life-threatening COVID-19 under a co-dominant model
Chr | Gene | GnomAD AF threshold | No. carriers of at least one (no. homozygous) pLOF variant | Joint analysis | Trans-ethnic meta-analysis | Trans-pipeline meta-analysis | ||
|---|---|---|---|---|---|---|---|---|
Cases (n = 3269) | Controls (n = 1373) | OR[95%CI] | P value | P value | P value | |||
14 | NPC2 | 0.01 | 28 (0) | 4 (0) | 5.41[1.8–16.4] | 5.8 × 10−4 | 2.1 × 10−3 | 3.3 × 10−4 |
3 | DLEC1 | 0.01 | 56 (0) | 16 (0) | 2.55[1.3–4.9] | 3.6 × 10−3 | 0.013 | 4.9 × 10−3 |
13 | NEK5 | 0.001 | 16 (0) | 0 (0) | 27.03[0.9–864.2] | 4.0 × 10−3 | 1.5 × 10−3 | 0.011 |
5 | CCNI2 | 0.01 | 19 (1) | 1 (0) | 7.15[1.2–43.1] | 4.1 × 10−3 | 4.1 × 10−3 | 5.0 × 10−3 |
22 | C22orf29 | 0.001 | 13 (0) | 0 (0) | 15.6[0.8–315.8] | 4.5 × 10−3 | 7.9 × 10−3 | 4.6 × 10−3 |
20 | DLGAP4 | 0.001 | 37 (0) | 3 (0) | 4.35[1.3–14.5] | 4.8 × 10−3 | 8.3 × 10−3 | 0.011 |