Table 2.
Exon-, UTR-, or Promoter-Overlapping CNVs in ASD-Associated and Candidate Genes
| Genes (MIM) | Families (n) | Families (%) | De Novo |
Inheritance |
Deletions | Duplications | Disrupted Elements | ||
|---|---|---|---|---|---|---|---|---|---|
| Maternal | Paternal | Unknowna | |||||||
| ANK2 (106410)b | 3 | 0.20 | 1 | 0 | 2 | 0 | 1 | 2 | exon, 3′ UTR, promoter |
| ASXL3 (615115) | 1 | 0.07 | 1 | 0 | 0 | 0 | 1 | 0 | exon |
| AUTS2 (607270)b | 2 | 0.14 | 0 | 2 | 0 | 0 | 1 | 1 | exon, promoter |
| CNTNAP2 (604569)c | 1 | 0.07 | 0 | 0 | 1 | 0 | 1 | 0 | exon |
| CNTN4 (607280) | 5 | 0.34 | 0 | 1 | 3 | 1 | 2 | 3 | exon, promoter |
| CTTNBP2 (609772)b | 1 | 0.07 | 0 | 1 | 0 | 0 | 0 | 1 | exon, 3′ UTR |
| CYFIP1 (606322) | 9 | 0.61 | 2 | 3 | 2 | 2 | 5 | 4 | exon |
| GABRB3 (137192)b | 1 | 0.07 | 0 | 0 | 0 | 1 | 0 | 1 | 5′ UTR |
| GIGYF1 (612064)d | 2 | 0.14 | 0 | 1 | 1 | 0 | 2 | 0 | whole gene, GNB2 (MIM: 139390) |
| KCNMA1 (600150)b,c | 1 | 0.07 | 0 | 1 | 0 | 0 | 0 | 1 | 5′ UTR + |
| MACROD2 (611567)c | 6 | 0.41 | 1 | 2 | 1 | 2 | 6 | 0 | 3′ UTR,4 promoter, 5′ UTR, exon |
| MIB1 (608677)b | 1 | 0.07 | 0 | 0 | 0 | 1 | 0 | 1 | exon, 3′ UTR, miR133 |
| MYO9B (602129)b | 1 | 0.07 | 0 | 0 | 0 | 1 | 1 | 0 | exon, 3′ UTR |
| NCKAP1 (604891) | 1 | 0.07 | 0 | 0 | 0 | 1 | 1 | 0 | whole gene deleted |
| NRXN1 (600565)c | 7 | 0.48 | 0 | 3 | 2 | 2 | 7 | 0 | exon, 5′ UTR, promoter |
| NRXN3 (600568)c | 1 | 0.07 | 0 | 0 | 0 | 1 | 1 | 0 | exon |
| RBFOX1 (605104)c,e | 6 | 0.41 | 1 | 3 | 2 | 0 | 3 | 3 | exon, promoter |
| SLC5A12 (612455) | 1 | 0.07 | 0 | 1 | 0 | 0 | 0 | 1 | exon, 3′ UTR |
| SHANK2 (603290)f | 1 | 0.07 | 0 | 1 | 0 | 0 | 0 | 1 | exon, promoter, DHCR7 (MIM: 602858) |
| Total | 51 | 3.48 | 6 | 19 | 14 | 12 | 32 | 19 | – |
A list of all candidate genes with >50 kb CNVs overlapping a functional region (all events overlap at least one exon, the 5′ UTR, and the promoter or the 3′ UTR). In total, 3.48% of families carry one of these events. Most of the CNVs are inherited.
The parent(s) did not have biomaterials available for genotyping, and the mode of inheritance could not be assessed.
Gene listed as a haploinsufficiency gene in Huang et al.54 No information was available for RBFOX1.
Several families have CNVs in the intronic regions in this gene.
Both parents carry the deletion in a heterozygous state, and the child is a heterozygote. It is not possible to identify the parent of origin.
Families with deletions in the 3′ UTR contain unaffected children with this deletion.
Duplication also encompasses DHCR7. Disruptive mutations in this gene are known to cause ID and Smith-Lemli-Opitz syndrome (MIM: 270400).