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Table 2 List of pathogenic CNVs

From: Genomic imbalances defining novel intellectual disability associated loci

Patients Gender Alteration (Hg19) Type Size (Mb) Genes Key gene(s) involved Associated syndrome Phenotype overlap Inheritance Confirmation Array platform Ref
R1 Male arr 1p36.23-p36.21(8,593,674-15,396,672)x1dn del 6.7 86 ANGPTL7, CASZ1, MAD2L2, RERE de novo NP 1
R2 Male arr 2p13.1-p13.3(70,894,906-74,986,518)x1dnc del 4 62 CYP26B1, EXOC6B de novo NP 1 Wen J, 2013
R3 Male arr 3q22.1-q23(131,415,639-141,618,552)x1dn del 1.020 65 FOXL2 BPES Yes (eye features) de novo NP 1
C1 Male arr 5p15.33-p15.32(204,849-5,014,883)x1 del 4.81 30 TERT [CTNND2 not involved] ND NP 2
R4 Male arr 6q25.3(156,012,754-158,804,494)x1dnc del 2.6 14 ARID1B Coffin-Siris syndrome Yes de novo NP 1 Santen GW, 2013
C2 Male arr 7q11.23(72,721,760-74,140,846)x1 del 1.419 28 BAZ1B, STX1A, WBSCR22, ELN Williams-Beuren syndrome Partially ND NP 2
R5 Female arr 8p23.1(7,039,276-12,485,558)x1dn del 5.5 70 SOX7, GATA4 8p23.1 deletion syndrome Yes (cardiac) de novo NP 1
C3 Male arr 11q24.2-q25(125,232,584-134,446,160)x1dn del 9.214 54 KIRREL3, ETS1, FLI1, KCNJ1, KCNJ5, RICS Partially de novo qPCR 2
R6 Female arr 12q24.21-q24.22(115,505,500-117,441,683)x1dnc del 0.2 10 MED13L Yes de novo qPCR 1 Adegbola A, 2015
C4 Male arr 16p11.2(29,674,336-30,198,123)x1dn del 0.524 29 KCTD13 16p11.2 deletion syndrome de novo NP 2
C5 Male arr 17q21.31(43,710,371-44,215,352)x1 del 0.505 8 CRHR1, MAPT, STH, and part of the KIAA1267 (KANSL1) 17q21.31 deletion syndrome (Koolen-De Vries syndrome) ND NP 3
C6 Male arr 22q11.21(18,894,835-21,505,417)x1 del 2.611 59 TBX1 22q11 deletion syndrome ND NP 2
C7 Male arr 22q13.3(49,513,903-51,178,264)x1 del 1.664 39 SHANK3 22q13.3 deletion syndrome (Phelan-McDermid syndrome) Partially ND NP 2
C8 Male arr 1q21.1q21.2(146,106,723-147,830,830)x3dn dup 1.7 17 HYDIN2, PRKAB2 1q21.1 duplication syndrome e Partially de novo qPCR 4
R7 Male arr 1q21.1(145,883,119-148,828,690)x3pat dup 2.5 23 HYDIN2, PRKAB2, GJA5 1q21.1 duplication syndrome e Yes paternal NP 1
R8 Male arr 12q24.21(116,408,736-116,704,303)x3dnc dup 0.3 2 MED13L Yes de novo qPCR 1 Adegbola A, 2015
C9 Male arr 13q12.12-q34(23,749,431-115,083,342)x2.15a dup 91.33 ## Trisomy 13 (mosaicism) Yes ND Karyotyped 2
C10 Female arr 15q11.2-q13.1(22880274–29,331,964)x3mat dup 6.45 111 CYF1P1, NIPA2, NIPA1, MKRN3, NDN, MAGEL2, SNURF/SNRPN, UBE3A GABRB3 15q11-q13 duplication syndromeb Yes maternal NP 2
C11 Female arr 16p13.11(15,034,010-16,199,882)x3 dup 1.166 11 NDE1 16p13.11 duplication syndrome e ND NP 5
R9 Male arr 16p13.11(15,421,671-16,443,968)x3mat dup 1 19 NDE1 16p13.11 duplication syndrome e Yes maternal NP 1
R10 Male arr 16p13.11(15,484,180-16,308,344)x3mat dup 0.8 9 NDE1 16p13.11 duplication syndrome e Yes maternal NP 1
C12 Male arr 21q11.2-q22.11(14,417,523-34,894,625)x3 dup 20.47 110 DSCR1, DSCR2, DSCR3, DSCR4, APP No ND NP 2
R11 Male arr Xp11.22(53,569,653-53,769,748)x2mat dup 0.2 3 HUWE1 Yes maternal qPCR 1
R12 Male arr Xq28(152,348,378-155,228,013)x2dn dup 2.8 78 MECP2 MECP2 duplication syndrome Yes de novo NP 1
R13 Male arr Xq28(153,130,545-153,602,293)x2mat dup 0.5 16 MECP2 MECP2 duplication syndrome Yes maternal NP 1
R14 Male arr 9q34.13-q34.3(135,767,911-141,153,431)x3dn dup 5.516 135 EHMT1, RXRA, GRIN1, UAP1L1 9q34 duplication syndrome Partially de novo NP 1
arr 14q32.31-q32.33(102,959,110-104,578,612)x3dn dup 1.620 22 MARK3, KLC1, EIF5 de novo NP 1
arr 14q32.33(105,104,831-106,531,339)x3dn dup 1.427 24 de novo NP 1
  1. Patients R1 to R14: from research cohort; Patients C1 to C12: from clinical cohort; NP Not performed, ND Not determined; (a): mosaicism; (b) methylation status for SNRPN is normal (studied by MLPA); (c): Published in detail elsewhere; (d): karyotype revealed a balanced translocation between chromosomes 13 and 14, resulting in mosaic trisomy 13; (e): Other causes of disease were not excluded therefore the variant might not explain the total phenotypic presentation. Array platform 1: Agilent 180 K; 2: KaryoArray®v3.0 (Agilent 8x60k); 3: Affymetrix CytoScan HD array; 4: Affymetrix CytoScan 750 K; 5: Agilent Whole Genome 244 K