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Table 3 List of likely pathogenic CNVs

From: Genomic imbalances defining novel intellectual disability associated loci

Patients Gender Alteration (Hg19) Type Size (Kb) Genes Relevant genes involved Confirmation Inheritance DGV controls DECIPHER Array platform Ref
C13 Male arr 1q43-q44(240,043,427-249,233,096)x1dn f del 3.7 18 AKT3 qPCR de novod No 250,152, 250,915 (smaller) 1 Lopes F, et al., 2019
R15 Female arr 1q43-q44(243,552,007-243,738,675)x1dn f del 0.19 2 AKT3 qPCR de novod No 252,432 (smaller) 2 Lopes F, et al., 2019
C14 Male arr 1q43q44(243,592,147-243,749,968)x1pat f del 0.16 2 AKT3 qPCR paternal No 252,432 (smaller) 1 Lopes F, et al., 2019
R16 Female arr 2q11.2-q12.2(101,756,265-106,265,018)x1dn del 4500 24 MAP4K4, FHL2, POU3F3, CNOT11 qPCR de novo No 251,756 2
R17, R18e Male, Female arr 7q33(133,176,651-135,252,871)x1mat f del 2076 23 AGBL3, CNOT4, CALD1, EXOC4 qPCR maternala No 256,036 2 Lopes F, et al., 2018
R19 Female arr 10q26.3(131,374,701-132,030,468)x1dn del 600 3 EBF3 qPCR de novo 3/6564b No 2 Lopes F et al., 2017
C15 Male arr 17p11.2(16,757,564-17,178,161)x1mat del 420 5 COPS3 NP maternala No No 3
arr 17p11.2(18,478,816-21,255,056)x1mat del 2770 36 EPN2, RNF112, ULK2, ALDH3A2, AKAP10, B9D1 NP maternala No 340,692 (smaller)
R20 Female arr 20q13.12-q13.13(43,283,820-48,850,844)x1dn del 5500 88 KCNB1, PIGT, CTSA, SLC2A10, ARFGEF2 NP de novo No 309 2
C16 Female arr 1p22.1p21.3(92,227,986-98,689,243)x3mat dup 6461 44 FAM69A, TGFBR3, GLMN, EVI5, RPL5, MTF2, DR1, ABCA4, ABCD3, CNN3, PTBP2, DPYD qPCR maternala No 318,358 1
C17,C18e Male, Male arr 7q33(134,598,205-134,815,177)x3mat f dup 216 2 CALD1, AGBL3 qPCR maternala No No 1 Lopes F, et al., 2018
R21 Female arr 9q33.2-q33.3(123,525,064-127,187,619)x4dn tri 3600 52 CRB2, LHX2, LHX6, DENND1A, STRBP, RAB14, GSN, PSMB7, ZBTB26 qPCR de novo No No 2
C19 Female arr 9q34.3(140540819–140,659,057)×3mat dup 0.118 2 EHMT1 NP maternal 1/2504 (smaller) No 1
R22, R23e Male, Male arr Xq24(119,592,606-119,904,981)x2mat dupc 300 4 CUL4B, LAMP2, C1GALT1C1, MCTS1 qPCR maternal No No 2
C20 Male arr Xq26.3(135,293,144-135,863,290)x2mat dup 570 9 ARHGEF6, CD40LG, BRS3, MAP7D3 qPCR maternal No No 3
  1. Patients R15 to R23: from research cohort; Patients C13 to C20: from clinical cohort; NP Not performed; (a): inherited from an affected parent; (b): doubt regarding the quality of the call in these controls; (c) duplication may disrupt gene if located in tandem; (d) paternity and maternity confirmed; (e): siblings; (f): family described elsewhere. Array platform 1: Affymetrix Cystoscan 750 K; 2: Agilent 180 K; 3: KaryoArray®v3.0 (Agilent 8x60k)