<p>Supplementary Table 2: Full list of high stringency genic CNV calls (2 or more algorithms), with no overlapping calls in 2,357 POPGEN and OHI controls, and <50% overlap in DGV. Coordinates refer to Human Genome Build36/hg18. Algorithms used include iPattern (IPN), Genotyping Console (GTC) and BirdSuite (BS). CNVs validated by qPCR are indicated by bold type. Ancestry is European unless otherwise stated in the footnotes. A list of all calls, including lower stringency calls is available from the corresponding author.</p><p>ID Cytoband Start Stop Size C Algorithms # of Probes Genes MIM #; N Associated V pathology</p><p>A217# 1q24.3 170,174,1 170,226,179 52,069 g BS,IPN|GTC 41 DNM3 11 a i n</p><p>A217# 1q31.3 195,206,3 195,222,522 16,181 L BS,IPN|GTC 19 CFHR5 61480;neph 42 o ropathy s s</p><p>A86 1q41 218,154,6 218,179,823 25,154 G BS,IPN 18 SLC30A10 613280; 70 a hypermanga i n- esemia n with dystonia, polycythem ia & cirrhosis</p><p>A62 2p25.1 10,208,86 10,474,077 265,213 L BS,IPN|GTC 213 HPCAL1,C2orf48 5 o s s</p><p>A187 2p23.3 25,717,73 25,777,692 59,958 g BS,IPN|GTC 33 DTNB 5 a i n</p><p>A156 2q21.2 133,600,5 133,728,969 128,442 L BS,IPN|GTC 90 NCKAP5 28 o s s</p><p>A116 3p25.3 11,451,72 11,466,305 14,578 L BS,IPN|GTC 17 ATG7 * 8 o s s</p><p>A200 3p24.3 17,655,22 17,758,388 103,168 L BS,IPN|GTC 45 TBC1D5 1 o s s</p><p>A204 3q21.1 124,907,3 124,956,275 48,946 L BS,IPN|GTC 28 MYLK 613780; 30 o familial s thoracic s aortic aneuysm 7</p><p>A27 3q25.32 158,558,2 158,639,900 81,619 G BS,IPN|GTC 57 VEPH1,PTX3 82 a i n</p><p>A184 3q28 192,624,9 192,672,766 47,867 L BS,IPN|GTC 37 PYDC2 00 o s s</p><p>A217 3q28 193,415,1 193,427,820 12,628 G BS,IPN|GTC 35 FGF12 93 a i n</p><p>A217 3q28 193,430,5 193,452,431 21,886 L BS,IPN|GTC 16 FGF12 46 o s s</p><p>A6 4p12 47,881,69 47,910,404 28,706 L BS,IPN|GTC 86 TEC 9 o s s</p><p>A213 5q12.3 63,974,15 64,240,025 265,870 G BS,IPN|GTC 143 FAM159B,CWC27,SREK1IP1 6 a i n</p><p>A23 6p25.1 5,170,870 5,308,007 137,138 L BS,IPN|GTC 95 FARS2,LYRM4 614946 o (FARS2) ; s Combined s oxidative phosphoryla tion deficiency 14</p><p>A44 6p24.1,6p24.2 11,192,62 11,233,071 40,449 L BS,IPN|GTC 23 LOC221710,HERV-FRD 3 o s s</p><p>A196 6p22.3 17,763,62 17,862,652 99,029 G BS,IPN|GTC 54 NUP153 4 a i n</p><p>A83 6q15 88,234,01 88,350,126 116,111 G BS,IPN|GTC 62 SLC35A1,RARS2 603585 6 a (SLC35A1) i ; n Congenital disorder of glycosylati on, type IIf</p><p>A50 7q11.22 68,391,49 68,846,056 454,564 G BS,IPN|GTC 235 AUTS2 607373; 3 a autism i susceptibilit n y 8</p><p>A103 7q35 145,687,3 145,707,079 19,727 L BS,IPN|GTC 19 CNTNAP2 610042; 53 o cortical s dysplasia- s focal epilepsy syndrome; Pitt- Hopkins Like syndrome1;</p><p>612100; autism susceptibilit y 15</p><p>A210 7q36.2 152,909,7 153,711,379 801,622 G BS,IPN|GTC 571 DPP6 612956; 58 a Ventricular i fibrillation, n paroxysmal familial, 2 A35$ 7q36.2 153,462,8 153,529,856 67,048 L BS,IPN|GTC 38 DPP6 09 o s s</p><p>A41 8p23.1 9,948,345 9,980,334 31,990 L BS,IPN|GTC 28 MSRA o s s</p><p>A196 9p11.2-q12 45,506,51 65,370,766 19.9Mb L BS|GTC 55 FAM75A5,FAM75A7,FAM74A4,FAM7 6 o 4A2,FAM27A,KGFLP1 s s</p><p>A32 10p14 8,021,446 8,034,890 13,445 L BS,IPN 14 TAF3 o s s</p><p>A67% 10p11.21 35,393,77 35,496,363 102,593 L BS,IPN|GTC 45 CREM,CUL2 1 o s s</p><p>A67 10q22.1 74,184,90 74,230,349 45,445 L BS,IPN|GTC 26 CCDC109A 5 o s s</p><p>A210 11p14.1 28,105,47 28,135,299 29,828 L BS,IPN|GTC 17 METTL15 2 o s s</p><p>A196 11q13.4 73,617,08 73,947,977 330,895 G BS,IPN|GTC 230 P4HA3,PPME1,KCNE3,LIPT2,PGM2L1 3 a i n</p><p>A21 11q14.1 83,108,46 83,378,706 270,241 G BS,IPN|GTC 208 DLG2 6 a i n</p><p>A16 12q24.11 108,087,8 108,127,535 39,659 L BS,IPN|GTC 28 ACACB 77 o s s</p><p>A136 12q24.22 115,655,3 115,797,029 141,658 G BS,IPN|GTC 89 C12orf49,RNFT2,HRK 72 a i n</p><p>A213 12q24.33 130,105,7 130,333,801 228,008 G BS,IPN|GTC 187 LOC116437,GPR133 94 a i n</p><p>A94 13q21.33 69,452,46 69,471,066 18,606 L BS,IPN|GTC 11 KLHL1 1 o s s</p><p>A182 14q23.3 66,274,49 66,631,750 357,252 l BS,IPN|GTC 142 GPHN 252150; 9 o Molybdenu s m cofactor s deficiency, type C</p><p>A83 14q31.1 78,548,11 78,587,995 39,879 L BS,IPN|GTC 35 NRXN3 7 o s s</p><p>A187 14q32.33 103,116,8 103,151,310 34,436 l BS,IPN|GTC 16 C14orf153 (APOPT1) 75 o s s</p><p>A23 15q21.3 52,531,91 52,555,069 23,155 L BS,IPN|GTC 16 UNC13C 5 o s s</p><p>A136 16p11.2 28,660,95 28,951,376 290,425 L BS,IPN|GTC 77 ATXN2L,ATP2A1,NFATC2IP,SPNS1, 613444; 2 o RABEP2,SH2B1,LAT,TUFM,CD19 16p11.2 s deletion s syndrome (220Kb);</p><p>601003 (ATP2A1); Brody myopathy;</p><p>610678 (TUFM); Combined oxidative phosphoryla tion deficiency 4;</p><p>613493 (CD19); Immunodefi ciency, common variable, 3</p><p>A67 16q12.1 47,911,71 48,519,007 607,296 G BS,IPN|GTC 456 C16orf78,ZNF423 614844 2 a (ZNF423); i Joubert n syndrome 19, Nephronop hthisis 14</p><p>A217# 17p12 12,238,67 12,985,028 746,356 g BS,IPN|GTC 563 ARHGAP44,MYOCD,FLJ34690,ELAC2 614731 3 a (ELAC2); i susceptibilit n y to hereditary prostate cancer 2</p><p>A44 17q21.31 39,578,59 39,756,006 177,413 G BS,IPN|GTC 77 C17orf65,ASB16,TMUB2,SLC25A39,U 179800 4 a BTF,RUNDC3A,SLC4A1,C17orf53,AT (SLC4A1); i XN7L3 Renal n tubular acidosis, distal, AD A162 17q23.3 58,985,82 58,999,732 13,908 l BS,IPN|GTC 11 DCAF7 5 o s s</p><p>A196 17q24.3 68,081,13 68,107,879 26,743 g IPN|GTC 18 FLJ26484,LOC100499467 7 a i n</p><p>A196 17q24.3 68,143,01 68,212,703 69,690 g BS,IPN|GTC 69 FLJ26484,SLC39A11 4 a i n</p><p>A79 17q25.3 74,912,21 75,225,624 313,407 G BS,IPN|GTC 81 hCG_1776007 8 a i n</p><p>A144 18q23 75,895,79 75,956,745 60,948 G BS,IPN|GTC 43 C18orf22 8 a i n</p><p>A153 18q23 75,895,79 75,956,745 60,948 G BS,IPN|GTC 43 C18orf22 8 a i n</p><p>A161 19p13.2 11,891,25 11,922,384 31,127 G BS,IPN 24 ZNF700 8 a i n</p><p>A62 21q22.11 31,680,65 31,991,168 310,512 G BS,IPN|GTC 201 TIAM1,SFRS15,SOD1 105400 7 a (SOD1); i Amyotrophi n c lateral sclerosis 1</p><p>A150a Xp22.11,Xp21.3 24,513,97 27,864,451 3,350,473 G BS,IPN|GTC 2105 MAGEB18,POLA1,PCYT1B,ARX,VE 310465 9 a NTXP1,SMEK3P,MAGEB10,MAGEB (POL1); N i 6,SCARNA23,DCAF8L2 syndrome; n 300419 (ARX); Mental retardation, X-linked 29 and others</p><p>A38b& Xq13.1 68,811,63 68,873,651 62,021 G BS,IPN|GTC 39 EDA 313500; 1 a Tooth i agenesis, n selective, X-linked 1</p><p>305100; Ectodermal dysplasia 1, hypohidroti c, X-linked</p><p>A67b Xq23 111,485,5 112,035,904 550,371 G BS,IPN|GTC 329 AMOT,ZCCHC16,LHFPL1 34 a i n aproband is male bproband is female</p><p>%:qPCR was attempted but was unable to validate this CNV</p><p>#:father from Pakistan, mother from Austria *: Ugandan</p><p>$:Egyptian</p><p>&: Turkish</p>