Table 1:

SKAT-O and burden analysis results for each gene, across cohort and coverage depth for mutation type

Depth of coverage	Gene	Number of Variants Tested	All rare		Number of Variants Tested	Rare CADD		Number of Variants Tested	Rare functional		Number of Variants Tested	Rare nonsynonymous		Number of Variants Tested	Rare loss-of-function
			SKAT-O	SKAT Burden		SKAT-O	SKAT Burden		SKAT-O	SKAT Burden		SKAT-O	SKAT Burden		SKAT-O	SKAT Burden
30x	McGill
	DNAJC13	143	0.727	0.494	37	0.905	1	47	0.845	0.647	44	0.899	0.800	NV	NV	NV
	EIF4G1	56	0.733	0.818	16	0.637	0.986	38	0.566	0.836	23	0.872	0.690	8	0.315	1
	GIGYF2	164	0.254	0.236	19	0.237	0.477	48	0.104	0.075	24	0.320	0.659	9	0.885	0.854
	HTRA2	13	0.592	0.341	3	0.798	0.798	7	0.292	0.513	2	0.223	0.223	1	0.611	0.611
	UCHL1	26	0.827	1	2	0.729	0.341	12	0.502	1	4	0.480	0.313	NV	NV	NV
	Columbia
	DNAJC13	97	0.709	0.493	28	0.344	0.206	32	0.500	0.317	31	0.594	0.393	NV	NV	NV
	EIF4G1	47	0.511	0.341	13	0.983	0.862	26	0.384	0.239	17	0.634	0.429	5	0.406	0.759
	GIGYF2	118	0.783	0.576	11	0.638	0.555	36	0.793	0.640	15	0.889	0.758	6	0.555	0.584
	HTRA2	10	0.276	0.323	2	0.344	0.774	6	0.835	0.835	2	0.344	0.774	NV	NV	NV
	UCHL1	19	0.751	0.715	3	0.928	0.771	9	0.891	0.741	3	0.781	0.547	NV	NV	NV
	Sheba
	DNAJC13	60	0.042	0.569	21	0.002	0.264	24	0.001	0.152	23	0.001	0.117	NV	NV	NV
	EIF4G1	34	0.703	0.489	14	0.544	0.678	18	0.617	0.583	13	0.635	0.688	2	0.103	0.103
	GIGYF2	88	0.278	0.203	8	0.837	0.709	35	0.198	0.232	8	0.654	0.473	14	0.165	0.159
	HTRA2	7	0.066	0.080	3	0.046	0.046	6	0.264	0.138	3	0.046	0.046	NV	NV	NV
	UCHL1	6	0.479	0.344	1	0.845	0.845	5	0.574	0.335	2	0.918	0.795	NV	NV	NV
	Merged
	DNAJC13	219	0.003	0.644	64	0.039	0.076	79	0.006	0.007	75	0.011	0.015	NV	NV	NV
	EIF4G1	104	0.669	0.850	31	0.035	0.172	62	0.365	0.239	42	0.238	0.712	7	0.208	0.150
	GIGYF2	284	0.246	0.787	32	0.634	0.449	94	0.322	0.418	38	0.682	0.840	24	0.310	0.302
	HTRA2	24	0.917	0.953	7	0.869	0.579	18	0.728	0.975	6	0.844	0.844	1	0.700	0.700
	UCHL1	39	0.406	0.817	5	0.429	0.376	18	0.601	1	6	0.181	0.280	NV	NV	NV
50x	McGill
	DNAJC13	82	0.602	0.544	23	0.399	1	28	0.410	0.833	25	0.416	0.860	NV	NV	NV
	EIF4G1	13	0.438	1	2	0.864	0.864	11	0.299	1	3	0.945	0.834	5	0.241	0.870
	GIGYF2	103	0.331	0.351	15	0.129	1	37	0.093	0.136	20	0.163	0.800	3	0.845	0.845
	HTRA2	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV
	UCHL1	17	0.435	0.288	2	0.715	0.715	4	0.282	0.193	4	0.282	0.193	NV	NV	NV
	Columbia
	DNAJC13	66	0.619	0.411	19	0.359	0.218	22	0.386	0.236	21	0.502	0.322	NV	NV	NV
	EIF4G1	7	0.568	0.590	NV	NV	NV	3	0.329	0.989	NV	NV	NV	1	0.331	0.331
	GIGYF2	70	0.370	0.228	9	0.453	0.264	25	0.308	0.181	11	0.618	0.434	2	0.202	0.135
	HTRA2	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV
	UCHL1	14	0.525	0.694	3	0.468	0.378	3	0.695	0.922	3	0.695	0.922	NV	NV	NV
	Sheba
	DNAJC13	38	0.043	0.151	14	2×10−4	0.132	15	5*10−4	0.139	14	2×10−4	0.132	NV	NV	NV
	EIF4G1	2	0.615	0.369	1	0.754	0.754	1	0.754	0.754	1	0.754	0.754	NV	NV	NV
	GIGYF2	40	0.626	0.416	5	0.607	0.444	19	0.510	0.335	7	0.780	0.608	NV	NV	NV
	HTRA2	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV
	UCHL1	4	0.546	0.395	1	0.847	0.847	2	0.917	0.792	2	0.917	0.792	NV	NV	NV
	Merged
	DNAJC13	146	0.018	0.561	42	0.154	0.128	52	0.078	0.053	48	0.099	0.072	NV	NV	NV
	EIF4G1	20	0.540	0.653	3	0.931	0.758	14	0.453	0.580	4	0.970	0.831	5	0.383	0.755
	GIGYF2	164	0.033	0.276	26	0.614	0.432	64	0.886	0.701	33	0.779	0.593	5	0.735	0.584
	HTRA2	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV	NV
	UCHL1	26	0.009	0.412	4	0.067	0.087	6	0.015	0.512	6	0.015	0.512	NV	NV	NV

Abbreviations: SKAT: Sequence Kernel Association Test; SKAT-O: Optimized Sequence Kernel Association Test; CADD: Combined Annotation Dependent Depletion; NV: No Variant