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Table 3 CNVs within genes

From: Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder

Cytoband Start Stop No. snp length (bp) CN Contained genes Frequency No. subjects No. affected No. families Predicted effect FBAT EMMAX Previous disease associations for gene
1p36.21 13171723 13218942 31 47220 0&1 LOC440563 Rare 38 13 15 Gene del 1 0.1887  
1q22 155152205 155162067 22 13287 3 MUC1, TRIM46 Amish specific 28 13 32 Partial gene dup 0.0711 0.1535 Kidney disease [42]
1q24.1 165644865 165649715 9 4851 1 ALDH9A1 Very rare 17 7 12 Exonic del 1 0.1434  
2q31.1 176929113 177000696 86 71584 3 EVX2, HOXD10, HOXD11, HOXD12, HOXD13, HOXD8, HOXD9 Amish specific 45 15 32 Gene dup 0.4122 0.9834 Limb and genital abnormalities [43,44]
2q37.3 241500674 241516094 20 24920 3 DUSP28, RNPEPL1 Very rare 74 13 43 Partial gene dup 0.4226 0.3229  
2q37.3 241482099 241516094 20 24920 3 ANKMY1, DUSP28, RNPEPL1 Very rare 31 7 23 Partial gene dup for ANKMY1 and RNPEPL1, gene dup for DUSP28 0.0007 0.3229  
3p21.2 51989546 51995419 11 10143 3 GPR62, PCBP4 Amish specific 72 17 47 Partial gene dup 0.0412 0.0238  
3p25.3 11411823 11414339 5 2517 0&1 ATG7 Rare 46 13 24 Intronic del 0.7557 0.7020 Frontotemporal dementia, Parkinsons disease [45]
3q29 193136358 193140348 9 3991 0&1 ATP13A4 Rare 41 9 18 Intronic del 0.7389 0.2519 Autism [46]
4q22.1 91907363 91913329 16 10710 1 FAM190A Amish Specific 34 6 21 Intronic del 0.0099 0.0794  
5q35.3 179221537 179238794 25 32170 3 LTC4S, MGAT4B, MIR1229, SQSTM1, MAML1 Amish specific 79 17 36 Partial gene dup for LTC4S and SQSTM1, gene dup for MGAT4B and MIR1229 0.6641 0.0973 Venous thromboembolism and ischaemic stroke [47], Paget disease of bone [48]
5q35.3 179211629 179231681 25 32170 3 LTC4S, MGAT4B, MIR1229 Amish specific 61 14 36 Gene dup 0.2513 0.0973 Venous thromboembolism and ischaemic stroke [47]
6p21.32 32610719 32614917 10 4199 1 HLA-DQA1 Rare 25 7 13 Exonic del 1 0.0574  
6p25.3 1612234 1620037 15 9536 3 FOXC1 Very rare 47 14 23 Exonic dup 1 0.5815 Axenfeld-Rieger anomaly [49]
6q26 163041460 163139315 64 99376 1 PARK2 Very rare 21 5 11 Exonic del 0.5637 0.5534 Parkinsons disease [50], Autism [51]
7q22.1 100968058 101063059 159 183210 3 EMID2 Rare 100 25 38 Exonic dup 0.0330 0.7031  
7q36.1 149461487 149516968 67 55482 3 SSPO, ZNF467 Amish specific 154 39 68 Partial gene dup 0.8907 0.1100  
8p21.3 21943602 22024523 80 62524 3 FAM160B2, HR, NUDT18 Amish specific 112 20 59 Partial gene dup for FAM160B2 and HR, gene dup for NUDT18 0.0284 0.9422 Alopecia universalis [52], Congenital Atrichia [53]
8p22 15947559 16023673 118 76115 1 MSR1 Rare 19 3 7 Partial gene del 0.0833 0.6317 Prostate cancer [54]
8p22 15419777 15432653 24 21108 1 TUSC3 Very rare 19 3 7 Intronic del 0.0833 0.6317 Intellectual disability [55]
9q34.11 130497180 130518716 22 29513 3 SH2D3C, TOR2A Amish specific 59 7 33 Partial gene dup for TOR2A, gene dup for SH2D3C 0.0116 0.4779  
10q11.21 45222200 45359483 125 151274 3 TMEM72-AS1 Rare 38 11 15 Partial gene dup 0.4386 0.5237  
10q21.3 68239474 68422442 209 182969 1 CTNNA3 Very rare 19 5 10 Partial gene del 0.6547 0.5957 Arrhythmogenic right ventricular cardiomyopathy [56]
11p11.2 45916436 45931646 24 29093 3 C11orf94, MAPK8IP1, PEX16 Amish specific 46 8 28 Partial gene dup for MAPK8IP1 and PEX16, gene dup for C11orf94 0.0197 0.0402 Diabetes type 2 [57], Zellweger syndrome [58]
11p15.4 8959020 8964938 11 5919 1 ASCL3 Very rare 28 6 12 Gene del 0.4795 0.3681  
13q34 112712459 112726336 26 26199 3 SOX1 Amish specific 109 23 53 Gene dup 0.0254 0.0749 Neuronal development [59]
13q34 114518789 114530659 31 17552 3 GAS6 Very rare 92 21 45 Partial gene dup 0.6946 0.6193  
14q23.2 63957653 63962909 10 6398 1 PPP2R5E Very rare 23 5 12 Intronic del 0.2568 0.1877  
15q11.2 24345146 24496990 76 152110 1 PWRN2 Rare 48 20 15 Gene del 0.1967 0.4189 Prader-Willi region [60]
15q26.1 90615898 90636762 28 26809 3 IDH2, ZNF710 Amish specific 27 8 13 Partial gene dup 0.7389 0.3569 D-2-hydroxyglutaric aciduria, type II [61]
16p12.1 27337036 27350687 15 20228 0&1 IL4R Very rare 31 9 15 Exonic del 0.7812 0.1062  
17p13.3 811982 1183612 665 456481 3 ABR, BHLHA9, MIR3183, NXN, TIMM22, TUSC5 Very rare 23 3 12 Partial gene dup for NXN and TUSC5, gene dup for ABR, BHLHA9, MIR3183 and TIMM22 0.6547 0.3319  
18q23 77150335 77162816 40 24952 3 NFATC1 Amish specific 41 13 23 Exonic dup 0.8273 0.1415 Tricuspid atresia [62]
18q23 76725624 76767375 35 41752 3 SALL3 Very rare 37 11 30 Gene dup 0.1336 0.0864  
18q23 77241092 77251061 21 16450 3 NFATC1 Amish specific 31 13 19 Exonic dup 0.3938 0.1313  
21q22.3 44822871 44868895 35 46025 3 SIK1 Rare 95 22 38 Gene dup 0.2800 0.5553  
  1. CNVs shown are rare in controls (present in fewer than 5% of controls. Rare: <5%, Very rare: <1%, Amish Specific: not found in controls), and common in the Amish (present in more than 5% of individuals). Contained genes shows all genes in CNV, disease genes are highlighted in bold. FBAT and EMMAX p-values for association analysis for Bipolar disorder are included, p<0.05 are in bold.