Table III.
Summary of validated copy number variations (CNVs) in spontaneous premature ovarian failure (POF) cases.
| Locus | Position (hg19) | Length (kb) | CN | Probe count | Genes within CNV | Cases (n = 301) | Controls (n = 3188) | CNV carriers among cases (%) | CNV carriers among controls (%) | Case ID |
|---|---|---|---|---|---|---|---|---|---|---|
| 1q43 | chr1: 240341241–240561727 | 189.9 | 1 | 37 | FMN2 | 1 | 1 | 0.33 | 0.03 | Case1 |
| 2p13.11 | chr2: 73828493–73900329 | 71.8 | 1 | 13 | ALMS1, NAT8 | 1 | 0 | 0.33 | 0 | Case2 |
| 2q33.1 | chr2: 200250898–201845999 | 1595.1 | 3 | 451 | SATB2, FTCDNL1, C2orf69, TYW5, C2orf47, SPATS2L, KCTD18, SGOL2, AOX1, AOX2P, BZW1, CLK1, PPIL3, NIF3L1, ORC2, FAM126B | 1 | 1 | 0.33 | 0.03 | Case3 |
| 6q27 | chr6: 170713690–170890384 | 176.7 | 3 | 70 | FAM120B, PSMB1, TBP, PDCD2 | 1 | 1 | 0.33 | 0.03 | Case4 |
| 7p14.3 | chr7: 33639870–33730376 | 90.5 | 1 | 30 | BBS9 | 1 | 10 | 0.33 | 0.31 | Case5 |
| 9q22.31 | chr9: 95063947–95179836 | 115.9 | 1 | 70 | NOL8, CENPP, OGN, OMD | 1 | 1 | 0.33 | 0.03 | Case6 |
| 10q26.3c | chr10: 135256762–135379710 | 122.9 | 1 | 70 | CYP2E1, SYCE1 | 2 | 3 | 0.66 | 0.09 | Case7 Case8 |
| 12q24.31 | chr12: 125260645–125321461 | 60.8 | 3 | 13 | SCARB1 | 1 | 1 | 0.33 | 0.03 | Case9 |
| 15q25.2c | chr15: 83213963–84811815 | 1597.8 | 1 | 325 | CPEB1, AP3B2, FSD2, WHAMM, HOMER2, FAM103A1, C15orf40, BTBD1, TM6SF1, HDGFRP3, BNC1, SH3GL3, ADAMTSL3, EFTUD1P1 | 1 | 0 | 0.33 | 0 | Case10 |
| 16p13.12 | chr16: 13889247–14163635 | 274.3 | 3 | 35 | ERCC4 | 1 | 0 | 0.33 | 0 | Case11 |
| 17q12 | chr17: ×–36220373 | 1404.8 | 3 | 327 | ZNHIT3, MYO19, PIGW, GGNBP2, DHRS11, MRM1, LHX1, AATF, ACACA, C17orf78, TADA2A, DUSP14, SYNRG, DDX52, HNF1B | 1 | 8 | 0.33 | 0.25 | Case12 |
| 22q13.2 | chr22: 43122720–43500212 | 377.5 | 1 | 54 | ARFGAP3, PACSIN2, TTLL1 | 1 | 3 | 0.33 | 0.09 | Case13 |
| Xp22.31d | chrX: 6516735–8138080 | 1618.3 | 3 | 111 | HDHD1, STS, VCX, PNPLA4 | 2 | 21b | 0.66 | 0.66 | Case14 Case15 |
| Xq12 | chrX: 66905875–67475065 | 569.2 | 3 | 20 | AR, OPHN1 | 1 | 1 | 0.33 | 0.03 | Case16 |
| Xq22.1-q24 | chrX: 99931059–120328627 | 20397.6 | 1 | 2001 | SYTL4…GLUD2a | 1 | 0 | 0.33 | 0 | Case17 |
All the discrete regions have been validated by qPCR, except for 20 Mb Xq22.1-q24 deletion; del, deletion; dup, duplication; CN, copy number.
a>100 genes in total, first and last genes in the region are indicated.
bSTS gene is not covered in any of these 21 control individuals with overlapping Xp22.31 duplications.
cFirst reported by McGuire et al (2010).
dFirst reported by Quilter et al (2010); loci indicated in bold were chosen for subsequent whole-exome sequencing in corresponding CNV carriers.