Table 5.

Top Gene-level Association Signals for Genes with Multi-allelic Sites. We performed simple burden, SKAT, and VT tests under the two different minor allele frequency cutoffs, 0.01 and 0.05. No results were significant under the threshold $\alpha =2.5\times {10}^{-6}$. For each rare-variant test performed, we show the test statistics, p-values, the number of variant sites, and the number of multi-allelic variant sites for the top 3 signals.

Gene	Statistic	p-Value	Number of Variant Site	Number of Multi-allelic Site	Number of Multi-allelic Site with Rare Variant	Gene	Statistic	p-Value	Number of Variant Site	Number of Multi-allelic Site	Number of Multi-allelic Site with Rare Variant
Burden Test with MAF < 1%						Burden Test with MAF < 5%
MLKL	16.81	4.1 × 10−5	16	8	4	PTPN22	13.49	0.00024	19	10	3
DMBX1	13.11	0.00029	4	2	2	CROCC	11.14	0.00085	80	11	8
BRD3	10.73	0.0011	5	6	4	HLA-DQA1	10.25	0.0014	6	15	0
SKAT Test with MAF < 1%						SKAT Test with MAF < 5%
ABTB1	1,654,137.32	5.5 × 10−5	12	6	5	ABTB1	1,834,395.76	0.00015	12	6	5
SEMA7A	1,056,004.78	0.00032	5	2	1	DTNBP1	4,098,263.16	0.00049	7	6	5
METTL8	1,075,541.99	0.00036	6	15	8	NRBF2	1,454,883.06	0.00074	3	4	2
VT Test with MAF < 1%						VT Test with MAF < 5%
TTC15	21.98	1.9 × 10−5	17	23	9	TTC15	21.98	2.46 × 10−5	17	23	9
MLKL	16.81	0.00031	16	8	4	WNK1	16.11	0.00049	41	25	8
ARHGEF40	15.08	0.00078	26	4	2	MLKL	15.71	0.00068	16	8	4