Table 5.
SKAT-O results of common variants: common variants are defined as MAF > 0.05 in gnomAD.
| Gene | Locus | p value—WES | Variants tested | p value—WGS | Variants tested |
|---|---|---|---|---|---|
| AMOT | chrX:112,774,503–112,840,815 | 8.21E−04 | 1 | 0.849 | 6 |
| CEP290 | chr12:88,049,016–88,142,088 | 1.88E−04 | 3 | 0.064 | 3 |
| CTDSP1 | chr2:218,399,755–218,405,941 | 8.82E−04 | 2 | 0.392 | 3 |
| DNAJA4 | chr15:78,264,086–78,282,196 | 2.37E−04 | 2 | 0.296 | 7 |
| GABRE | chrX:151,953,124–151,974,676 | 2.49E−04 | 1 | 0.339 | 6 |
| HHAT | chr1:210,328,252–210,676,296 | 6.39E−04 | 3 | 0.576 | 5 |
| HJURP | chr2:233,836,702–233,854,535 | 8.49E−04 | 7 | 0.592 | 10 |
| MEFV | chr16:3,242,028–3,256,627 | 7.18E−04 | 8 | 0.388 | 12 |
| MRGPRX3 | chr11:18,120,955–18,138,480 | 6.07E−04 | 3 | 0.808 | 6 |
| MYO5B | chr18:49,822,789–50,195,147 | 2.72E−04 | 5 | 0.263 | 14 |
| NEK10 | chr3:27,110,904–27,369,392 | 8.52E−04 | 3 | 0.092 | 8 |
| NR0B2 | chr1:26,911,489–26,913,975 | 5.91E−04 | 1 | 0.83 | 3 |
| PLEKHM3 | chr2:207,821,288–208,025,527 | 3.48E−04 | 2 | 0.826 | 10 |
| SAG | chr2:233,307,816–233,347,055 | 3.35E−04 | 3 | 0.527 | 3 |
| TRMT9B | chr8:12,945,673–13,029,777 | 6.22E−05 | 8 | 0.627 | 40 |
| WDR61 | chr15:78,283,235–78,299,609 | 5.98E−04 | 1 | 0.414 | 2 |
| WDR87 | chr19:37,884,932–37,906,677 | 8.81E−05 | 4 | 0.198 | 13 |
| ZNF571 | chr19:37,562,392–37,594,790 | 8.60E−04 | 3 | 0.203 | 5 |
| ZNF573 | chr19:37,738,302–37,779,590 | 7.08E−04 | 2 | 0.148 | 3 |
All genes were tested in the WES dataset; only the top-ranked genes (p < 0.001) were tested in the WGS dataset as a replication set. Common variant SKAT-O analyses were not weighted by MAF. In the ‘Locus’ column, ‘chr’ refers to chromosome.