Table 2.
Gene-based tests of rare nonsynonymous variants in RA
| GENE | Chr | Gene-based test * | ||
|---|---|---|---|---|
| N marker | SKAT-O (nonburden test) P value | SCORE_seq (burden test) | ||
| P value | ||||
| VSTM1 | 19 | 7 | 4.55 × 10−3 | 7.80 × 10−4 |
| KPRP | 1 | 8 | 6.38 × 10−3 | 6.51× 10−3 |
| C6orf99 | 6 | 5 | 0.05155 | 0.01669 |
| PARD3 | 10 | 21 | 0.14496 | 0.01887 |
| PYGL | 14 | 10 | 0.02287 | 0.02057 |
| ARHGAP26 | 5 | 9 | 0.01939 | 0.02114 |
| NCF2 | 1 | 8 | 0.02574 | 0.02159 |
| CCR6 | 6 | 7 | 0.01131 | 0.02776 |
| TRAF6 | 11 | 8 | 0.04621 | 0.02876 |
| GRIN2B | 12 | 6 | 0.20806 | 0.02966 |
| SNTB1 | 8 | 6 | 0.00987 | 0.03395 |
| PTCD3 | 2 | 11 | 0.14462 | 0.03772 |
| CA8 | 8 | 3 | 0.17982 | 0.03792 |
| NRXN3 | 14 | 8 | 0.12536 | 0.03905 |
| CPEB4 | 5 | 7 | 0.05104 | 0.04010 |
| CTNNA3 | 10 | 16 | 0.10312 | 0.04079 |
| KRT24 | 17 | 5 | 0.02866 | 0.04837 |
*We defined rare nonsynonymous variants as MAF <5% in both cases and controls. We selected 347 genes with two or more rare nonsynonymous variants for gene-based tests. RA, rheumatoid arthritis; Chr, chromosome; Nmarker, number of rare nonsynonymous variants for each gene.