Table 1.
Atypical 7q11.23 Copy Number Variants (CNVs).
| Participant | CNV | Start | End | CNV size | Array | Genes within CNV |
|---|---|---|---|---|---|---|
| Atyp Del1 | Loss | 74,304,574 | 74,719,013 | 414,439 bp | CGH + SNP (GenomeDx) | CLIP2a; GTF2IRD1; GTF2Ib |
| Atyp Del2 | Loss | 74,023,916 | 74,731,820 | 707,904 bp | SNP Array 6.0 (Affymetrix) | ELNa; LIMK1; EIF4H; MIR590; LAT2; RFC2; CLIP2; GTF2IRD1; GTF2Ib |
| Atyp Del3 | Loss | 73,330,491 | 73,813,707 | 483,216 bp | CMA + HR + SNP v9.1.1 (Agilent) | FKBP6; FZD9; BAZ1B; BCL7B; TBL2; MLXIPL; VPS37D; DNAJC30; BUD23; STX1A; MIR4284; ABHD11-AS1; ABHD11; CLDN3; CLDN4 |
| Atyp Dup1 | Gain | 74,002,716 | 74,232,208 | 229,492 bp | CGH + SNP 4x180K (Agilent) | ELN; LIMK1; EIF4H; MIR590; LAT2; RFC2c |
| Atyp Dup2 | Gain | 73,326,323 | 73,944,794 | 618,471 bp | OmniExpress PIs (Illumina) | FKBP6; FZD9; BAZ1B; BCL7B; TBL2; MLXIPL; VPS37D; DNAJC30; BUD23; STX1A; MIR4284; ABHD11-AS1; ABHD11; CLDN3; CLDN4; METTL27; TMEM270 |
| Gain | 74,375,400 | 74,730,726 | 355,326 bp | CLIP2c; GTF2IRD1; GTF2Ib | ||
| Atyp Dup3 | Gain | 73,528,186 | 74,662,079 | 1,133,893 bp | SNP Array 6.0 (Affymetrix) | FZD9d; BAZ1Bd; BCL7B; TBL2; MLXIPL; VPS37D; DNAJC30; BUD23; STX1A; MIR4284; ABHD11-AS1; ABHD11; CLDN3; CLDN4; METTL27; TMEM270; ELN: LIMK1; EIF4H; MIR590; LAT2; RFC2; CLIP2; GTF2IRD1; GTF2Ic |
All coordinates are based on GRCh38/hg38 assembly.
aGenes that are partially deleted.
bA portion of this gene lies within a low copy repeat and therefore the exact deletion or duplication breakpoint cannot be determined by diagnostic microarray or real-time qPCR. All of the unique portion of the gene lies within the CNV.
cGenes that are partially duplicated.
dThese genes were demonstrated to be duplicated using real-time qPCR and the Infinium HumanMethylation450k array analysis, although they were not included in the duplication interval on the original diagnostic microarray.