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Table 2 Gene-based tests of rare nonsynonymous variants in RA

From: Targeted exon sequencing fails to identify rare coding variants with large effect in rheumatoid arthritis

GENE Chr Gene-based test*
Nmarker SKAT-O (nonburden test)Pvalue SCORE_seq (burden test)
Pvalue
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
  1. *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.