Table 1 De novo variant enrichment analysis for each functional class in 90 VOGM trio cases and control cohorts

VOGM cases, N = 90							Controls, N = 1798
	Observed		Expected		Enrichment	p		Observed		Expected		Enrichment	p
	N	Rate	N	Rate	Enrichment	p		N	Rate	N	Rate	Enrichment	p
All genes (N = 19,347)							All genes (N = 19,347)
Total	107	1.19	99.7	1.11	1.07	0.25	Total	1839	1.02	1977.1	1.10	0.93	1.00
Syn	28	0.31	28.2	0.31	0.99	0.54	Syn	492	0.27	559.8	0.31	0.88	1.00
T-Mis	46	0.51	49.4	0.55	0.93	0.71	T-Mis	949	0.53	979.3	0.54	0.97	0.84
D-Mis	22	0.24	13.4	0.15	1.65	0.02	D-Mis	248	0.14	266.7	0.15	0.93	0.88
LoF	11	0.12	8.7	0.10	1.27	0.26	LoF	150	0.08	171.3	0.10	0.88	0.95
Protein altering	79	0.88	71.5	0.79	1.11	0.20	Protein altering	1347	0.75	1417.3	0.79	0.95	0.97
Protein damaging	33	0.37	22	0.24	1.5	0.02	Protein damaging	398	0.22	438	0.24	0.91	0.98
Loss-of-function intolerant genes (gnomADv2.1.1 pLI ≥ 0.9; N = 3,049)							Loss-of-function intolerant genes (gnomADv2.1.1 pLI ≥ 0.9; N = 3,049)
Total	22	0.24	23.9	0.27	0.92	0.68	Total	456	0.25	473.5	0.26	0.96	0.83
Syn	4	0.04	6.7	0.07	0.59	0.90	Syn	115	0.06	133.4	0.07	0.86	0.96
T-Mis	6	0.07	10.9	0.12	0.55	0.96	Mis	233	0.13	213.5	0.12	1.08	0.12
D-Mis	9	0.10	4.2	0.05	2.12	0.03	D-Mis	75	0.04	84.5	0.05	0.88	0.87
LoF	3	0.03	2.1	0.02	1.4	0.36	LoF	33	0.02	42.2	0.02	0.78	0.94
Protein altering	18	0.20	17.2	0.19	1.05	0.45	Protein altering	341	0.19	340.2	0.19	1	0.53
Protein damaging	12	0.13	6.4	0.07	1.88	0.03	Protein damaging	108	0.06	126.7	0.07	0.85	0.96

N Number of de novo variants (DNVs), Rate: number of DNVs per subject; Enrichment: ratio of observed to expected numbers of DNVs; Syn synonymous variants, D-mis damaging missense variants as predicted by MetaSVM or MPC ≥2, T-mis tolerated missense variants as predicted by MetaSVM or MPC <2, LoF loss-of-function variants comprised of premature termination, frameshift, or splice-site variants; Significance threshold determined by upper cumulative quantile (one-sided) of Poisson distribution. Not adjusted.

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