Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

Reggiani, Claudio; Coppens, Sandra; Sekhara, Tayeb; Dimov, Ivan; Pichon, Bruno; Lufin, Nicolas; Addor, Marie-Claude; Belligni, Elga Fabia; Digilio, Maria Cristina; Faletra, Flavio; Ferrero, Giovanni Battista; Gerard, Marion; Isidor, Bertrand; Joss, Shelagh; Niel-Bütschi, Florence; Perrone, Maria Dolores; Petit, Florence; Renieri, Alessandra; Romana, Serge; Topa, Alexandra; Vermeesch, Joris Robert; Lenaerts, Tom; Casimir, Georges; Abramowicz, Marc; Bontempi, Gianluca; Vilain, Catheline; Deconinck, Nicolas; Smits, Guillaume

doi:10.1186/s13073-017-0452-y

Table 1 Description of the 29 patients having deletions in the DLG2 7-9 region

From: Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

Patient ID	Type of CNV	DLG2 CNV hg19 coordinates	CNV size (Mb)	DLG2 deleted features	Gender	Other rare CNVs	Inheritance of DLG2 variant	Neurodevelopmental phenotype
Patient 1 317136	Del	Chr11:84245639-84772741	0.52	Exons 7–8; HPin7	Male	0	Inherited from an unaffected mother	C, B
Patient 2 317185	Del	Chr11:84334015-84797219	0.46	Exon 7; HPin7	Male	0	Inherited from an unaffected mother	C, B
DECIPHER 248668	Del	Chr11:84548697-84628963	0.08	Intron 7	Male	32	Unknown	C
DECIPHER 256592	Del	Chr11:84456097-84607440	0.15	Intron 7	Male	1^a	Unknown	C, B
DECIPHER 263216	Del	Chr11:84003279-84276072	0.27	Exons 8–9; HPin8	Male	0	Inherited from a parent with same phenotype	Unknown
DECIPHER 270892	Del	Chr11:84108622-84334253	0.23	Exon 8; HPin8	Male	0	Inherited from normal parent	C, B
DECIPHER 272251	Del	Chr11:83805117-84215024	0.41	Exons 9–13; HPin8	Female	3^b	Inherited from an unaffected mother	C, B, P
DECIPHER 273969	Del	Chr11:83996254-84214903	0.22	Exon 9; HPin8	Male	0	Unknown	Unknown
DECIPHER 278011	Del	Chr11:84367238-84721340	0.35	Exon 7; HPin7	Male	1^c	De novo constitutive	C
DECIPHER 281197	Del	Chr11:84085773-84477088	0.39	Exon 8; HPin7-8	Male	0	Inherited from an unaffected mother	C, B
DECIPHER 284804	Del	Chr11:84046644-84539636	0.49	Exon 8; HPin7-8	Male	0	De novo constitutive	C, B
DECIPHER 286641	Del	Chr11:84291759-84477088	0.19	Intron 7; HPin7	Male	1^d	Inherited from an unaffected mother	Unknown
DECIPHER 288027	Del	Chr11:84046530-84454687	0.41	Exon 8; HPin7-8	Male	1^e	Inherited from an unaffected mother	C, B
DECIPHER 288501	Del	Chr11:84334017-84595634	0.26	Intron 7; HPin7	Female	1^f	Unknown	Other
DECIPHER 288842	Del	Chr11:84334017-84595634	0.26	Intron 7; HPin7	Unknown	1^g	Unknown	Other
DECIPHER 289734	Del	Chr11:84595575-84907579	0.31	Exons 5–7	Unknown	2^h	De novo constitutive	C, B
DECIPHER 292620	Del	Chr11:84046614-84214762	0.17	Intron 8; HPin8	Female	0	Unknown	C
DECIPHER 300042	Del	Chr11:84046614-84419502	0.37	Exon 8; HPin8	Unknown	0	Unknown	C
DECIPHER 300109	Del	Chr11:84419443-84581292	0.16	Intron 7; HPin7	Unknown	0	Inherited from a mother of unknown phenotype	C
DECIPHER 300111	Del	Chr11:84367238-84539665	0.17	Intron 7; HPin7	Unknown	0	Inherited from a mother of unknown phenotype	C
1339 [10]	Del	Chr11:83595987-84489649	0.89	Exons 8–18; HPin7-8	Unknown	1ⁱ	De novo constitutive	C, B, E
L4 [48]	Del	Chr11:84003321-84266329	0.26	Exons 8–9; HPin8	Unknown	Unknown	Unknown	P
L5 [46]	Del	Chr11:83945764-84214964	0.27	Exons 9–11; HPin8	Male	Unknown	Inherited from an unaffected mother	P
L6 [47]	Del	Chr11:83795102-84165325	0.37	Exons 9–13; HPin8	Unknown	Unknown	De novo constitutive	P
L7 [47]	Del	Chr11:84328458-84548416	0.22	Intron 7; HPin7	Unknown	Unknown	De novo constitutive	P
L8 [49]	Del	Chr11:84143697-84312722	0.17	Exon 8; HPin8	Unknown	1^j	Unknown	P
L9 [49]	Del	Chr11:84111384-84354568	0.24	Exon 8; HPin8	Unknown	1^k	Unknown	P
L11 [44]	Del	Chr11:83961633-84633847	0.67	Exons 8–11; HPin7-8	Female	Unknown	Inherited from an unaffected mother	P
L13 [44]	Del	Chr11:84375859-84521180	0.145	Intron 7; HPin7	Male	Unknown	Unknown	P

Neurodevelopmental phenotype abbreviations: C cognitive, B behavioral, P psychiatric, E epilepsy; we used patients’ DECIPHER id whenever available; this is the case for the two ULB patients and the 18 public DECIPHER patients. The 21st entry is identified by the reported id number in Vulto-van Silfhout et al. [10]. We provide inside square brackets references for the other eight patients found in the literature (L4-9, L11, L13). See Additional file 1: Tables S7–S11 for a more detailed description. HPin7 and HPin8 are names given to the new DLG2 functional regions described in this work (see text)
^a30-kbp dup on chrY. Genes: AKAP17A, ASMT
^b225-kbp dup and 278-kbp dup on chr9, 148-kbp dup on chr11. Genes: TRPM3, TMEM2, EHF
^c300-kbp del on chr17 variant inherited from normal parent. Genes: SLC39A11
^d290-kbp dup on chr17 inherited from mother. 22 genes
^e130-kbp dup on chr7 inherited from mother. Gene: AKAP9
^f180-kbp del on chr1. Genes: INPP5B, MTF1, SF3A3
^g541-kbp del on chr16. 28 genes
^h191-kbp del on chr1 and 101-kbp del on chr12; both inherited from mother. Genes: SUMF1, PIK3C2G, RERGL
ⁱ5-Mbp dup on chr15; de novo. Several genes
^j41-kbp del on chr1. Gene: DNAJC6
^k23-kbp dup on chr20. No gene

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ISSN: 1756-994X

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