Table 1.
Genes disrupted by chromosomal rearrangements*
| Cat | ID | Dx | ChrA | ChrB | Disrupted | Fisher’s Exact P‡ | Function |
|---|---|---|---|---|---|---|---|
| 1 | DGAP201 | ASD | 7q11.22 | 7q36.3 | AUTS2 | 5.6E-04 | Unknown |
| 1&4 | NDR27031 | NDD | 3q13.32 | 18q21.2 | TCF4 | 6.2E-04 | Transcription factor |
| 1 | DGAP093 | NDD | Xp22.13 | 19p13.3 | CDKL5 | 7.2E-02 | Protein kinase |
| 1 | DGAP157 | NDD | 3p13 | 10q21.2 | FOXP1 | 4.5E-02 | Transcription factor |
| 1&4 | NDR25941 | ASD | 12p13.1 | 12q21.31 | GRIN2B | 7.9E-02 | Glutamate receptor |
| 1 | DGAP189 | NDD | 11p13 | 12p12.1 | SOX5 | 8.4E-02 | Transcription factor in embryonic development |
| 2 | DGAP232 | ASD | 9p11.2 | 15q11.2 | SNURF-SNRPN | 1.1E-13 | Genomic Imprinting in Angelman – PWS region |
| 2&4 | DGAP155 | ASD | 9q34.3 | 11p11.2 | EHMT1 | 3.3E-07 | Histone Methyltransferase |
| 2 | DGAP142 | ASD | 2q23.1 | 22q13 | MBD5 | 3.1E-05 | Methylation binding |
| 2 | DGAP211 | ASD | 2q33.1 | 6q16.3 | SATB2 | 1.1E-03 | Transcriptional regulation and Chromatin remodeling |
| 3 | DGAP148 | NDD | Xp11.4 | 11q24.2 | KIRREL3 | 1.6E-04 | Cell adhesion |
| 3 | DGAP154 | NDD | Xq22 | 17p13.3 | SMG6 | 5.9E-04 | Nonsense mediated decay |
| 3 | NDR26867 | ASD | 3q25.31 | 14q11.2 | CHD8 | 2.4E-02 | Chromatin remodeling |
| 3 | DGAP125 | NDD | 7q32.1 | 19q13.11 | ZNF507 | 8.0E-02 | Zinc Finger |
| 3 | DGAP132** | NDD | 5q12.2 | 7q21.3 | PON3 | 1.5E-01 | Lactonase |
| 3 | AC02-0053 | ASD | 6q16.1 | 9q21.13 | GNA14 | 2.7E-01 | G-protein signaling |
| 3 | DGAP131 | NDD | 1p22.3 | 5q33 | ZNHIT6 | 2.7E-01 | Zinc finger protein |
| 3 | DGAP193 | ASD | 2p22.3 | 2q31.3 | SPAST | 2.7E-01 | Membrane trafficking |
| 3&4 | DGAP143 | NDD | 6q22.1 | 6q27 | PDE10A | 5.2E-03 | Phosphodiesterase |
| 3&4 | DGAP171 | NDD | 17p13.2 | 18p11.21 | C18orf1 | 3.2E-02 | Unknown |
| 3&4 | DGAP180** | NDD | 2q32 | 11q14 | ZNF804A | 4.7E-02 | Zinc finger protein |
*
BCA-disrupted genes individually implicated by case-control CNV burden at p < 0.10 or by a minimum of 3 CNVs in cases with none in controls are provided. See Table S1 and SI for all subjects and phenotypes and Table S2 for CNV counts on all subjects.
‡
Fisher’s exact test p-value from comparison of CNV burden between NDD cases and controls.
Cat = disruption category, Dx = diagnosis
ASD = autism spectrum disorder
NDD = other neurodevelopmental disorders
ChrA and ChrB = sequenced chromosomal sub-band containing the BCA
**
BCA inherited from similarly affected parent.