List of de novo and likely deleterious brain malformation CNVs ordered by their cytogenetic bands.

“Known/Novel” refers to whether the CNV has been previously observed to be de novo in patients with one or more of the three brain malformations (Known) or not (Novel). While some of the “Novel” CNVs may previously have been implicated in other disorders, they are novel for the malformations used in this study. Double asterisks denote de novo CNVs at least 500 kb with high pathogenicity scores. Single asterisks denote de novo CNVs less than 500 kb with slightly lower pathogenicity scores. While deletions of 7q36.3 have been linked to ACC, duplications have not which is why it is “Novel”. Similarly, deletion 9p23-p22.3, which has not been observed in ACC, overlaps a known ACC region with duplications (see Table S9). Many de novo CNVs in ACC were found to overlap de novo CNVs observed in autism. All CNVs listed are de novo except for the following five: 9p23-p22.3, 9q34.3, Xq28 (1223-0) for which inheritance could not be determined; 16p13.11 which was paternally inherited and uncovered a maternally inherited nonsense pathogenic mutation in NDE1; and Xq28 (LR02-148) which was maternally inherited. While patient 1574-0 has one large de novo deletion on 1q41-q42.13 that overlaps a well-known ACC interval, the second de novo deletion on 1q31.2-q31.3 is also large and likely to be deleterious.