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. 2017 Nov 30;9:105. doi: 10.1186/s13073-017-0488-z

Table 1.

Pathogenic CNVs (n = 41) identified in 39 unrelated participants with schizophrenia annotated by IQ group

No. ID IQ group Sex Chr Cytoband Start (hg 19) Size (bp) CN Segdupsa Previously publishedb Genes (n) Selected candidate gene(s)d
1 2 Average M 1 1q21.1 145,760,806 2,083,985 Gain • • 17 BCL9, GJA5, PRKAB2, GJA8, PDZK1
2 3 Average F 1 1q21.1 145,932,468 1,898,716 Gain • • 15 BCL9, GJA5, PRKAB2, GJA8, PDZK1
3 562f Mod ID F 2 2p16.3 51,066,869 563,162 Loss •c 1 NRXN1
4 570 BL M 2 2p16.3 51,181,653 189,279 Loss •c 1 NRXN1
5 7f Average M 2 2q13 111,388,632 1,727,361 Gain • • 9 ANAPC1, BCL2L11, MERTK
6 8 Average M 2 2q13 111,388,632 1,727,361 Loss • • 9 ANAPC1, BCL2L11, MERTK
7 9 NVLD M 2 2q13 111,388,632 1,727,361 Gain • • 9 ANAPC1, BCL2L11, MERTK
8 396 NVLD M 3 3p26.1 4,418,429 277,309 Loss 3 SUMF1, ITPR1
9 13 NVLD M 3 3q13.31 113,825,760 2,062,410 Loss • 6 LSAMP, DRD3, ZBTB20, GAP43
10 452 Mild ID M 3 3q27.1-q27.2 184,400,855 1,580,956 Loss 17 TRA2B
11 565e,g BL F 5 5p15.33-5p15.2 113,577 10,191,390 Loss 83 IRX1, IRX2, IRX4, NDUFS6, SLC6A3, NSUN2, MTRR, CCT5
12 17 Average F 5 5p15.33-p15.32 1,811,574 3,687,431 Loss • 7 IRX1, IRX2, IRX4, NDUFS6
13 247 Mild ID F 6 6p25.3-p25.1 149,661 6,836,705 Loss • 35 FOXC1, GMDS, NRN1, TUBB2B
14 565e,g BL F 6 6q26-q27 163,617,482 7,302,001 Gain 59 RNASET2, TBP
15 206 BL F 7 7q22.2-q31.1 105,517,719 10,037,597 Loss • 34 COG5, DOCK4, FOXP2, GPR85, IMMP2L, LAMB1, NRCAM, PIK3CG, PNPLA8
16 115 BL F 8 8p23.3-p23.1 158,062 6,830,865 Loss • 21 ANGPT2, CLN8, CSMD1, DLGAP2, MCPH1
17 40 Average M 10 10q11.22-q11.23 46,485,761 5,173,684 Gain • • 42 CHAT, ERCC6, GDF2, GPRIN2, MAPK8, SLC18A3
18 569 Mild ID M 13 13q14.13-q14.3 46,589,256 6,220,619 Loss • 59 HTRA2, SUCLA2, ITMB2, RB1
19 48 BL M 15 15q11.2-q13.1 20,181,700 6,498,447 Gain • • 121 CYFIP1, GABRB3, GABRA5, GABRG3, MAGEL2, NDN, UBE3A
20 556 Mild ID M 15 15q11.2-q13.1 22,770,422 5,757,338 Gain • 116
21 427 NVLD F 15 15q11.2-q13.1 23,290,799 5,353,780 Gain • 115 GABRB3, GABRA5, GABRG3, MAGEL2, NDN, UBE3A
22 49 NVLD M 15 15q11.2-q13.1 23,641,514 5,432,624 Gain • • 106
23 50 Average M 15 15q11.2-q13.1 23,641,514 4,892,894 Gain • • 101
24 52j Mod ID F 15 15q13.2-q13.3 30,821,637 1,690,584 Loss • • 8 CHRNA7, OTUD7A, TRPM1
25 568 BL M 16 16p11.2 29,432,213 744,308 Loss • 40 DOC2A, MAPK3, PRRT2, QPRT, SEZ6L2, TBX6
26 55 Mild ID F 16 16p11.2 29,567,309 624,599 Gain • • 26
27 56f Mild ID F 16 16p11.2 29,567,309 659,635 Gain • • 33
28 57e Mild ID M 16 16p11.2 29,567,309 624,599 Gain • • 26
29 58 Mild ID M 16 16p11.2 29,567,309 659,635 Gain • • 33
30 277 Mild ID F 19 19p13.3-p13.2 2,754,548 9,685,341 Gain • 280 Various, including DNMT1, DOCK6
31 577 BL M 22 22q11.2 18,890,046 2,831,545 Loss • • 46 Various, including DGCR8
32 581 Mild ID F 22 22q11.2 18,890,046 2,831,545 Loss • • 46
33 582 Mild ID M 22 22q11.2 18,890,046 2,831,545 Loss • • 46
34 579 BL M 22 22q11.2 18,895,226 2,466,420 Loss • • 46
35 580i NVLD F 22 22q11.2 18,916,840 1,395,833 Loss • • 29
36 578h Mild ID F 22 22q11.2 20,717,655 1,087,074 Loss • 16 SNAP29, CRKL
37 271 Average F X X chr (46, XO) - 155,065,370 Loss 829 Various, including IL1RAPL1, SYN1
38 173 BL M X X chr (47, XXY) - 155,065,370 Gain • 829
39 57e Mild ID M X X chr (47, XXY) - 155,065,370 Gain • 829
40 194f Average M X Xp22.33-p22.2 2,400,835 11,075,950 Loss 40 NLGN4X, VCX, MID1
41 574f Mild ID F X Xp11.23-p11.22 48,178,414 4,508,892 Gain • 97 Various, including SHROOM4, WDR45, SYP, FTSJ1

aRare CNVs with one or both breakpoints falling within a segmental duplication are denoted by a bullet point

bAll CNVs with a bullet point in this column were previously published in Costain et al. (2013) [10] or cLowther et al. (2017) [35]

dThese candidate genes were previously reported in Costain et al. 2013 [10] or were based on a comparable method, i.e. genes associated with a neuropsychiatric or neurodevelopmental phenotype identified from a comprehensive literature search and/or in the Online Mendelian Inheritance in Man (http://www.omim.org/) database. Not every gene was systematically searched for those CNVs that overlapped ≥ 100 genes. Selected candidate genes are only reported once for recurrent CNVs

eThese individuals carry a second CNV classified as pathogenic

fThese individuals carry a second CNV classified as a VUS

gThese two CNVs are part of an unbalanced translocation

h,iThese are 22q11.2 deletions arising between low copy repeats: hB-D (atypical deletion) and iA-B (typical, short nested deletion), respectively

jCase 52 was identified to also have mosaic (6 of 24 cells) Turner syndrome by karyotype [10]

ID case identification number; Chr chromosome, CN copy number, Segdups flanking segmental duplication; Genes (n) number of RefSeq protein-coding genes overlapped, Average average IQ group, BL borderline IQ group, ID intellectual disability group (mild or moderate), NVLD non-verbal learning disability, M male, F female