Table II.

Additional clinically relevant CNVs identified in 12 of 19 intronic 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
I8	DD	Intron 21	3q27.1-q27.2	Loss	184,027,899	1,300	4	Unknown	EIF4G, CLCN2, CHRD, EPHB3, SENP2	VUS
I11c	ASD, heart defect, hip hypoplasia, clubfoot, absent radius	Intron 18	1q21.1d	Loss	144,986,396	998	20	Unknown	PDZK1	Pathogenic
I10	DD	Intron 18	4p16.2	Gain	3,185,517	155	3	de novo	HTT	VUS
I6	DD	Intron 5	1p21.2-p21.1	Gain	101,742,523	554	1	Unknown	OLFM3	VUS
I2c	DD	Intron 5	3p13	Loss	71,041,637	406	1	Unknown	FOXP1	Likely pathogenic
I1	DD, microcephaly	Intron 5	6q22.31-q23.2	Loss	125,993,504	5,900	22	Maternal	LAMA2	VUS
I13c	MCA	Intron 5	Mosaic trisomy chr 9	Gain	-	-	~800	Unknown	Various, including SETX	Pathogenic
I15	DD, ASD	Intron 5	11p13	Gain	33,008,222	557	6	Unknown	None	VUS
I4	Absent radius and thumb	Intron 5	15q13.1-q13.2	Gain	28,859,279	1,500	4	Unknown	APBA2	VUS
I14c	DD	Intron 5	15q11.2	Loss	22,669,082	998	5	Unknown	CYFIP1, NIPA2, NIPA1	Pathogenic
I17	DD	Intron 5	16p13.13	Loss	10,556,892	297	4	Paternal	None	VUS
I19	DD	Intron 5	11p15.5	Gain	1,222,378	318	4	Unknown	BRSK2	VUS

CNV, copy number variation; #, number; VUS, variant of unknown significance; DD, developmental delay; ASD, autism spectrum disorder; 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.

^cSubjects with CNVs classified as pathogenic. All other CNVs were classified as a variant of unknown significance.

^dOverlaps susceptibility locus for Thrombocytopenia-Absent radius syndrome (OMIM 274000).