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Table 1 Frequent CNVs associated with risk for neurodevelopmental disorders (NDDs)

From: Copy number variants (CNVs): a powerful tool for iPSC-based modelling of ASD

Locus Syndrome Rearrangements Position of critical region Key genes % in People with Autism
1q21.1   1q21.1; del and dup chr1:146,527,987-147,394,444 HYDIN2, PRKAB2, CHD1L, BCL9, GJA5, GJA8, GPR89B Del 0.039%, Dup 0.157% (Pinto et al., 2014) [19]
2p16.3   del chr2:50145643-51259674 NRXN1 Del 0.316% (Pinto et al., 2014) [19]
3q29   del chr3:195,720,167-197,354,826 DLG1 Del 0.005% (Malhotra et al., 2012) [20]
7q11.23 Williams-Beuren syndrome (WBS) del and dup chr7:72,744,915-74,142,892 CLDN3, CLDN4, GTF2, ELN, LIMK1, KCTD7, CLIP2, STX1A, Del .024%, Dup 0.097% (Pinto et al., 2014) [19]
9q34 Kleefstra syndrome del chr9:140,513,444-140,730,578 EHMT1 Del 0.049% (Pinto et al., 2014) [19]
15q11.2   BP1-BP2; del and dup chr15:22,805,313-23,094,530 CYFIP1 Del 0.09% (Malhotra et al., 2012) [20], Dup 0.94% (van der Zwaag et al., 2010) [21]
15q11-q13 Prader-Willi and Angleman’s syndromes BP2-BP3 chr15:29,161,368-32462776 UBE3A, ATP10A, GABARB3, GABARA5, GABARG3 Del 0.192% (Depienne et al., 2009) [22], Dup 0.255% (Pinto et al., 2014) [19]
15q13.3   BP4-BP5; del and dup chr15:32,017,070-32,453,068 CHRNA7 Del 0.157%, Dup 0.039% (Pinto et al., 2014) [19]
16p13.11   del and dup chr16:15,511,655-16,293,689 NDE1, MYH11 Del 0.137%, Dup 0.268% (Pinto et al., 2014) [19]
16p11.2   proximal (593 kb) del and dup chr16:29,650,840-30,200,773 KCTD13, ALDOA, CORO1A, MAPK3, TAOK2 Del 0.42%, Dup 0.39% (Malhotra et al., 2012) [20]
17q12 Renal cysts and diabetes syndrome (RCAD) del and dup chr17:34,815,904-36,217,432 NF1 Del 0.039%, Dup 0.020% (Pinto et al., 2014) [19]
22q11.2 Deletion known as DiGeorge syndrome, Velocardiofacial syndrome and 22q11.2 deletion syndrome del and dup chr22:19,037,332-21,466,726 TBX1, COMT, PI4KA, SEPT6 Del 0.059%, Dup 0.157% (Pinto et al., 2014) [19]
22q13 Phelan-McDermid syndrome (PMDS) del chr22:51113070-51171640 SHANK3 Del 0 .097% (Pinto et al., 2014) [19]