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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 1a 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 3b 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 1c 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 1d Inherited from an unaffected mother Unknown
DECIPHER 288027 Del Chr11:84046530-84454687 0.41 Exon 8; HPin7-8 Male 1e Inherited from an unaffected mother C, B
DECIPHER 288501 Del Chr11:84334017-84595634 0.26 Intron 7; HPin7 Female 1f Unknown Other
DECIPHER 288842 Del Chr11:84334017-84595634 0.26 Intron 7; HPin7 Unknown 1g Unknown Other
DECIPHER 289734 Del Chr11:84595575-84907579 0.31 Exons 5–7 Unknown 2h 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 1j Unknown P
L9 [49] Del Chr11:84111384-84354568 0.24 Exon 8; HPin8 Unknown 1k 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
  1. 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)
  2. a30-kbp dup on chrY. Genes: AKAP17A, ASMT
  3. b225-kbp dup and 278-kbp dup on chr9, 148-kbp dup on chr11. Genes: TRPM3, TMEM2, EHF
  4. c300-kbp del on chr17 variant inherited from normal parent. Genes: SLC39A11
  5. d290-kbp dup on chr17 inherited from mother. 22 genes
  6. e130-kbp dup on chr7 inherited from mother. Gene: AKAP9
  7. f180-kbp del on chr1. Genes: INPP5B, MTF1, SF3A3
  8. g541-kbp del on chr16. 28 genes
  9. h191-kbp del on chr1 and 101-kbp del on chr12; both inherited from mother. Genes: SUMF1, PIK3C2G, RERGL
  10. i5-Mbp dup on chr15; de novo. Several genes
  11. j41-kbp del on chr1. Gene: DNAJC6
  12. k23-kbp dup on chr20. No gene
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