Genomic imbalances defining novel intellectual disability associated loci

Lopes, Fátima; Torres, Fátima; Soares, Gabriela; Barbosa, Mafalda; Silva, João; Duque, Frederico; Rocha, Miguel; Sá, Joaquim; Oliveira, Guiomar; Sá, Maria João; Temudo, Teresa; Sousa, Susana; Marques, Carla; Lopes, Sofia; Gomes, Catarina; Barros, Gisela; Jorge, Arminda; Rocha, Felisbela; Martins, Cecília; Mesquita, Sandra; Loureiro, Susana; Cardoso, Elisa Maria; Cálix, Maria José; Dias, Andreia; Martins, Cristina; Mota, Céu R.; Antunes, Diana; Dupont, Juliette; Figueiredo, Sara; Figueiroa, Sónia; Gama-de-Sousa, Susana; Cruz, Sara; Sampaio, Adriana; Eijk, Paul; Weiss, Marjan M.; Ylstra, Bauke; Rendeiro, Paula; Tavares, Purificação; Reis-Lima, Margarida; Pinto-Basto, Jorge; Fortuna, Ana Maria; Maciel, Patrícia

doi:10.1186/s13023-019-1135-0

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 novo^d	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 novo^d	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, R18^e	Male, Female	arr 7q33(133,176,651-135,252,871)x1mat ^f	del	2076	23	AGBL3, CNOT4, CALD1, EXOC4	qPCR	maternal^a	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	3/6564^b	No	2	Lopes F et al., 2017
C15	Male	arr 17p11.2(16,757,564-17,178,161)x1mat	del	420	5	COPS3	NP	maternal^a	No	No	3	–
C15	Male	arr 17p11.2(18,478,816-21,255,056)x1mat	del	2770	36	EPN2, RNF112, ULK2, ALDH3A2, AKAP10, B9D1	NP	maternal^a	No	340,692 (smaller)	3	–
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	maternal^a	No	318,358	1	–
C17,C18^e	Male, Male	arr 7q33(134,598,205-134,815,177)x3mat ^f	dup	216	2	CALD1, AGBL3	qPCR	maternal^a	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, R23^e	Male, Male	arr Xq24(119,592,606-119,904,981)x2mat	dup^c	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	–

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)

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