Table 2. Candidate regions and genes selected for QMPSF analysis.

Chromosomal location	Type	Candidate Genes	Pathways	Function	Evidence	Disorder	Selected references
2p16.3	loss	NRXN1	synapse formation and maintenance	cell adhesion molecule	CR	ASD, SZ, MR	1, 4, 7, 8, 10, 38, 39
2q12.3-q14.2	loss/gain	DPP10	neurotransmission	dipeptidyl peptidase	CR	ASD	4
2q33.3-q34	loss	ERBB4	synapse formation and maintenance	NRG1 receptor	CR, M	SZ	8
3p26-p25	loss/gain	CNTN4	synapse formation and maintenance	Axon-associated cell adhesion molecule	CR, M	ASD, MR	40, 41
3p26.1-p25.2	loss	GRM7	neurotransmission	glutamate receptor	CR	SZ	8
3q26.31	gain	NLGN1	synapse formation and maintenance	cell adhesion molecule	CR	MR	42
4p14-q21.1	gain	GABRG1, GABRA4, GABRA2	neurotransmission	GABA receptor subunits	CR	ASD	4, 43
5p13	loss	SLC1A3	neurotransmission	excitatory amino acid transporter	CR, M	SZ	8
7q31.1	loss	ST7	other	tumor suppressor	CR, M	ASD	4
7q35-q36	loss	CNTNAP2	synapse formation and maintenance	contactin associated protein	CR, M	ASD, SZ, MR, TS	44
8p22-p11	loss	NRG1	synapse formation and maintenance	signaling protein	CR	MR	45
8p23	gain	DLGAP2	neurotransmission	associated to NMDA receptor and K+ channels	CR	ASD	4
8q24-qter	gain	PTK2	neuronal migration and growth	focal adhesion kinase	CR	SZ	8
11q21	loss	DLG2	synapse formation and maintenance	synaptic scaffolding protein	CR	SZ	8
12q14.3	loss	GRIP1	neurotransmission	glutamate receptor interacting protein	CR	MR	1, 3
15q11-q14	gain	GABRA5, GABRB3, GABRG3	neurotransmission	GABA receptor subunits	CR	ASD, MR	46, 47
15q13	gain	APBA2	neurotransmission	synaptic exocytosis	CR	ASD, SZ	6, 10
15q13.3	loss	CHRNA7	neurotransmission	acetylcholine receptor	CR	MR	48
16p11.2	loss/gain	DOC2A	neurotransmission	neurotransmitter release regulation	CR	ASD, SZ	4, 6, 8, 31, 33
17q21	loss/gain	MAPT	other	microtubule associated protein	CR	MR	28, 30
22q11	loss	PRODH	neuromodulation	proline dehydrogenase	CR, M	ASD, SZ, MR	19
22q13	loss	SHANK3	synapse formation and maintenance	synaptic scaffolding protein	CR, M	ASD, MR	4, 24–26
Xp22.3	loss/gain	NLGN4	synapse formation and maintenance	cell adhesion molecule	CR, M	ASD, TS, MR	4, 49–52
Xp11.4	gain	TSPAN7	neuronal migration and growth	transmembrane component	CR, M	ASD, MR	4, 27
Xp11.4	loss	CASK	synapse formation and maintenance	synaptic scaffolding protein	CR	MR	2
Xp22.1-p21.3	loss	IL1RAPL1	other	interleukin receptor	CR, M	ASD, MR	4, 53
Xq25	gain	GRIA3	neurotransmission	Kainate receptor subunit	CR	MR	29
Xq28	gain	MECP2	other	methylated CpG binding protein	CR, M	MR	42, 54

CR: Chromosomal rearrangement, M: mutation, TS: Tourette syndrome