Table 1:

Effect-size of gene dosage measured by pLI on phenotypes in autistic probands from the SSC.

Phenotypic measurements	N	CNV variable	No adjustment for NVIQ			Adjustment for NVIQ
			β or OR	SE or 95%CI	p	β or OR	SE or 95%CI	p
Autism related symptoms
Regression	2,568	pLI DEL	0.86	0.75-0.95	8.4×10−3	0.8	0.70-0.89	1.9×10−4
		pLI DUP	0.99	0.92-1.04	0.65	0.96	0.90-1.02	0.19
Language and phonology
CTOPP(a)	1,988	pLI DEL	−0.08	0.02	5.5×10−4	−0.02	0.02	0.24
		pLI DUP	−0.02	0.02	0.25	0.006	0.01	0.66
Word delay	2,567	pLI DEL	1.16	1.07-1.27	5.0×10−4	1.12	1.03-1.22	0.01
		pLI DUP	1.03	0.98-1.09	0.24	1.02	0.96-1.08	0.6
Phrase delay	2,567	pLI DEL	1.04	0.98-1.09	0.42	0.95	0.87-1.04	0.25
		pLI DUP	1.06	1.00-1.14	0.08	1.03	0.96-1.11	0.46
Adaptive skills (VABS-II)
Total score(a)	2,569	pLI DEL	−0.07	0.02	3.1×10−5	−0.004	0.01	0.72
		pLI DUP	−0.03	0.01	2.6×10−3	−0.01	0.01	0.4
Daily living(a)	2,569	pLI DEL	−0.07	0.02	1.2×10−4	−0.004	0.01	0.8
		pLI DUP	−0.04	0.01	3.4×10−3	−0.01	0.01	0.38
Communication(a)	2,569	pLI DEL	−0.07	0.02	3.4×10−4	0.01	0.01	0.54
		pLI DUP	−0.04	0.01	4.5×10−3	−0.005	0.01	0.6
Socialization(a)	2,569	pLI DEL	−0.06	0.02	4.8×10−4	−0.01	0.01	0.67
		pLI DUP	−0.03	0.01	0.02	−0.004	0.01	0.66
Motor skills
Motor VABS-II(a)	919	pLI DEL	−0.11	0.04	4.1×10−3	−0.08	0.03	0.01
		pLI DUP	−0.07	0.02	1.3×10−3	−0.04	0.02	0.02
Gross motor VABS-II(a)	926	pLI DEL	−0.08	0.03	0.01	−0.07	0.03	0.02
		pLI DUP	−0.05	0.02	4.6×10−3	−0.04	0.02	0.03
Fine motor	923	pLI DEL	−0.1	0.04	0.01	−0.07	0.03	0.04
VABS-II(a)		pLI DUP	−0.06	0.02	8.8×10−3	−0.03	0.02	0.14
Onset for walking in months	2,550	pLI DEL	1.03	1.02-1.04	2.2×10−11	1.03	1.02-1.04	4.6×10−9
		pLI DUP	1.02	1.01-1.03	7.0×10−9	1.02	1.01-1.03	5.3×10−8
Delayed onset for walking(a)	2,564	pLI DEL	1.16	1.05-1.28	2.0×10−3	1.11	1.00-1.22	0.03
		pLI DUP	1.2	1.11-1.30	6.1×10−6	1.19	1.09-1.29	4.2×10−5
DCDQ score(a)	2,209	pLI DEL	−0.07	0.02	2.5×10−3	−0.03	0.02	0.16
		pLI DUP	−0.03	0.01	0.04	−0.01	0.01	0.33
Associated neurological condition
Non-febrile seizure	2,566	pLI DEL	1.12	1.01-1.23	0.02	1.07	0.96-1.17	0.19
		pLI DUP	1.04	0.95-1.11	0.3	1.02	0.94-1.09	0.63

^(a)phenotypic measures z-scored using normative data when available or computed using the full autistic proband group (Method in the online supplement). In bold: p-values significant above the statistical threshold (p ≤ 2.7×10⁻³). Effects in this table represent either the normalized β z-scores with their standard errors (SE) or an odds ratio (OR) with its 95% confidence interval (95%CI).

pLI: probability of being Loss-of-function Intolerant; pLI DEL or pLI DUP: deleted or duplicated point of pLI score; NVIQ: non-verbal intelligence quotient; CTOPP: Comprehensive Test of Phonological Processing; VABS-II: Vineland Adaptive behaviour Rating Scales - Second Edition; DCDQ: Developmental Coordination Disorder Questionnaire.