Table I.

Additional clinically relevant CNVs identified in 10 of 44 exonic NRXN1 deletion subjects

IDa	Main clinical features	NRXN1 deletion	Cytoband	CNV	Start (hg 19)	Size (kb)	# of genes	Inheritance	Protein-coding candidate genesb	Clinical laboratory classification
P44	ID, ASD, ADHD, ODD, anxiety, TS	Exon 20	X chr (47, XXX)	Gain	-	-	-	de novo	Various, including FMR1, MECP2, SYN1	Pathogenic
P43	DD	β promoter	Yp11.32-p11.2	Gain	10,863	4,459	-	de novo	Various, including	Pathogenic
			Yq11.21-q12	Loss	14,630,081	44,700	-		NLGN4Y
P41	DD	Exons 10–17	1q43	Gain	236,929,252	613	3	Unknown	MTR, RYR2	VUS
			15q13.1-q13.2c	Loss	28,940,069	184	9		APBA2, CHRFAM7A, TJP1	VUS
P40	DD	Exons 5-8	11p11.2-p11.12	Gain	48,088,592	831	8	Paternal	None	VUS
P39	DD, ASD	Exons 5-8	1q23.3	Gain	160,927,546	428	23	Unknown	USF1, PVRL4, PFDN2, PPOX, B4GALT3, ADAMTS4, NDUFS2, NR1I3, PCP4L1, MPZ, SDHC	VUS
P38	DD/ID, motor and speech delay, PDD, anxiety, failure to thrive	Exons 5-8	4q35.2	Loss	188,355,766	383	1	Unknown	None	VUS
P36	DD, motor and speech delay	Exons 5-10	19q13.43	Loss	57,656,482	794	3	Unknown	None	VUS
P13	DD, behaviour problems	exons 1-2	16p13.3	Gain	6,679,225	38	1	Unknown	RBFOX1	VUS
P10	DD, speech delay	αP and exons 1-4	8p23.3	Gain	843,413	750	4	Paternal	DLGAP2	VUS
P6	DD, behavioural problems, hypotonia, bilateral sensorineural loss	αP and exons 1-2	1p22.1	Gain	92,179,826	526	6	Unknown	TGFBR3	VUS
			3q29d	Loss	192,404,455	164	2	Unknown	FGF12	VUS
			7q31.2-q31.31	Gain	117,382,934	1,700	3	Unknown	CTTNBP2	VUS
			Xp22.23	Gain	1,588,945	777	4	Unknown	P2RY8, ASMT	VUS

CNV, copy number variation. #, number; VUS, variant of unknown significance; DD, developmental delay; ASD, autism spectrum disorder; PDD, pervasive developmental disorder; ID, intellectual disability; ADHD, attention deficit hyperactivity disorder; ODD, oppositional defiant disorder; TS, Tourette’s syndrome; MCA, multiple congenital anomalies.

^aThe subject ID’s match those found in Figure 1.

^bProtein coding genes known to be expressed and/or implicated in nervous system function or cardiac function based on literature search.

^cThis deletion is distal to the Prader-Willi/Angelman syndrome region but proximal to the 15q13.3 deletion syndrome region (OMIM 612001).

^dDoes not overlap the 3q29 microdeletion syndrome region associated with schizophrenia (OMIM 609425).