Table 2.
Frequently observed recurrent CNVs identified among clinical populations referred for CMA testinga.
| CNVb | Copy Number | Syndrome | Size | Genomic Coordinates (hg19) |
|---|---|---|---|---|
|
Highly Penetrant Phenotype
| ||||
| 7q11.23 (ELN) | deletion | Williams | 1.4 Mbc | chr7:72744455-74142513 |
| 8p23.1 (SOX7, CLDN23) | deletion | 3.6 Mb | chr8:8119296-11765719 | |
| 8p23.1 (SOX7, CLDN23) | duplication | 3.6 Mb | chr8:8119296-11765719 | |
| 15q11.2q13 BP2-3d (UBE3A) | deletion | Prader-Willi or Angelman | 4.8 Mb | chr15:23758391-28557186 |
| 17p11.2 (RAI1) | deletion | Smith-Magenis | 3.5 Mb | chr17:16757112-20219651 |
| 17p11.2 (RAI1) | duplication | Potocki-Lupski | 3.5 Mb | chr17:16757112-20219651 |
| 17q21.31 (MAPT, KANSL1) | deletion | Koolen-de Vries | ||
| 22q11.2 (TBX1, HIRA) | deletion | DiGeorge/Velo-cardio-facial | 2.9 Mb | chr22:18661726-21561514 |
|
Variable Clinical Phenotype | ||||
| 1q21.1 (GJA5) | deletion | 0.8 Mb | chr1:146577487-147394506 | |
| 1q21.1 (GJA5) | duplication | 0.8 Mb | chr1:146577487-147394506 | |
| 7q11.23 (ELN) | duplication | 1.4 Mb | chr7:72744455-74142513 | |
| 15q11.2q13 BP2-3c (UBE3A) | duplication | 4.8 Mb | chr15:23758391-28557186 | |
| 15q13.3 BP4-5 (KLF13, CHRNA7) | deletion | 1.3 Mb | chr15:31137105-32445408 | |
| 15q13.3 BP4-5 (KLF13, CHRNA7) | duplication | 1.3 Mb | chr15:31137105-32445408 | |
| 16p11.2 (TBX6) | deletion | 0.6 Mb | chr16:29649997-30199855 | |
| 16p11.2 (TBX6) | duplication | 0.6 Mb | chr16:29649997-30199855 | |
| 16p11.2 distal (SH2B1) | deletion | |||
| 16p11.2 distal (SH2B1) | duplication | |||
| 16p12.1 (CDR2, EEF2K) | deletion | |||
| 16p13.11 (MYH11) | deletion | |||
| 17q12 (HNF1B) | deletion | Renal cysts and diabetes | ||
| 17q12 (HNF1B) | duplication | |||
| 22q11.2 (TBX1, HIRA) | duplication | 2.9 Mb | chr22:18661726-21561514 | |
a
The list is divided into CNVs that have a highly penetrant phenotype and those with more variable phenotypic presentations. Within each category, the CNVs are listed in chromosomal order. The CNV list was compiled from multiple sources, but should not be considered exhaustive: DECIPHER syndrome list (https://decipher.sangeer.ac.uk/syndromes#overview), ClinGen pathogenic list (http://www.ncbi.nlm.nih.gov/dbvar, study ID nstd45) and additional references25,36-39
b
genes in CNV region included as landmarks for genomic location and are not necessarily known to be causative of phenotype
c
Mb, Megabase
d
BP, breakpoint