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Table 1 Pathogenic CNVs (n = 41) identified in 39 unrelated participants with schizophrenia annotated by IQ group

From: Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia

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
  1. aRare CNVs with one or both breakpoints falling within a segmental duplication are denoted by a bullet point
  2. bAll CNVs with a bullet point in this column were previously published in Costain et al. (2013) [10] or cLowther et al. (2017) [35]
  3. 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
  4. eThese individuals carry a second CNV classified as pathogenic
  5. fThese individuals carry a second CNV classified as a VUS
  6. gThese two CNVs are part of an unbalanced translocation
  7. h,iThese are 22q11.2 deletions arising between low copy repeats: hB-D (atypical deletion) and iA-B (typical, short nested deletion), respectively
  8. jCase 52 was identified to also have mosaic (6 of 24 cells) Turner syndrome by karyotype [10]
  9. 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
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