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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]