Table 1.

Gene panel association tests results

Dataset	Deletions overlapping 69 DD loci		Duplications overlapping 69 DD loci		LoF variants in 599 DDG2P genes		Missense variants (REVEL > 0.7) in 599 DDG2P genes		Synonymous variants in 599 DDG2P genes
Binary traits	OR	p value	OR	p value	OR	p value	OR	p value	OR	p value
In employment	0.728	3.356E−10	0.814	7.580E−7	0.907	5.778E−4	0.988	0.500	1.012	0.323
Have a degree	0.624	2.052E−28	0.748	6.684E−17	0.833	6.134E−15	0.925	1.368E−7	1.028	6.115E−3
Have an epilepsy diagnosis	1.689	2.179E−3	1.292	0.113	1.394	0.003	1.068	0.403	0.917	0.131
Diagnosed with child DD	1.588	1.827E−4	1.279	0.030	1.316	5.056E−4	1.123	0.031	1.018	0.645
Diagnosed with adult DD	1.502	1.359E−6	1.395	4.027E−6	1.158	7.061E−3	1.062	0.092	1.003	0.914
Is unable to work	1.921	1.093E−16	1.554	6.663E−10	1.344	8.573E−8	1.134	8.459E−4	0.977	0.403

Continuous traits	Beta	p value	Beta	p value	Beta	p value	Beta	p value	Beta	p value
Fluid intelligence	−0.592	3.834E−20	−0.347	2.534E−11	−0.159	1.152E−6	−0.089	1.207E−5	0.002	0.865
Number of years in education	−1.139	7.878E−30	−0.755	1.496E−19	−0.391	4.589E−12	−0.189	1.323E−7	0.064	0.009
Income	−0.346	1.850E−45	−0.217	1.042E−26	−0.127	1.599E−20	−0.058	2.675E−11	0.012	0.040
Reaction time	0.199	1.086E−25	0.079	6.277E−7	0.043	8.179E−5	0.013	0.060	−0.005	0.290
Pairs test score	0.285	1.345E−5	0.315	7.174E−9	0.122	9.928E−4	0.055	0.019	−0.022	0.172
Townsend deprivation index	0.527	8.628E−19	0.485	9.962E−23	0.279	5.596E−17	0.090	1.855E−5	0.020	0.160
Age left education	−0.214	2.158E−5	−0.218	4.345E−7	−0.110	2.892E−4	−0.044	0.025	0.003	0.806
Height	−1.608	1.474E−36	−0.613	7.254E−9	−0.449	4.809E−10	−0.251	3.725E−8	0.044	0.164
Reported a mental health issue	0.071	1.629E−3	0.023	0.222	0.041	1.047E−3	0.015	0.053	−0.001	0.848
Numeric memory score	−0.188	1.765E−6	−0.054	0.096	−0.068	1.032E−3	−0.025	0.053	−0.002	0.813
BMI	0.157	3.164E−15	0.112	1.766E−11	0.032	4.611E−3	0.016	0.024	−0.003	0.608
Number of children fathered	−0.216	1.048E−9	−0.100	6.985E−4	−0.069	1.135E−3	−0.018	0.168	−0.011	0.210
Number of pregnancies	−0.041	0.358	−0.039	0.292	−0.043	0.076	−0.024	0.120	0.007	0.499
Number of stillbirths	0.005	0.381	0.009	0.066	0.004	0.245	0.004	0.039	0.001	0.430

DD, developmental disorder; LoF, loss of function; OR, odds ratio; BMI, body mass index.

Twenty relevant phenotypes were tested in individuals in UK Biobank carrying deletions or duplications overlapping 69 known DD-associated loci or rare (n ≤ 5) LoF, missense (REVEL > 0.7), or synonymous variants in any of 599 known monoallelic DDG2P genes.