Table 2.
Description of whole-genome custom exon array confirmed CNV calls of interest
| SSC ID | Sex | Chromosome | Min. start | Min. size | Type | RefSeq gene (hg19) | Probes exon | Validation testa | DGV |
|---|---|---|---|---|---|---|---|---|---|
| De novo autosomal heterozygous: 26 common and 6 rare | |||||||||
| 11458 | M | 1q21.3 | 152573248 | 13 045 | Loss | LCE3C, LCE3B | 5 | D/− | Common |
| 11076 | M | 1q31.3 | 196711807 | 111 947 | Gain | CFH, CFHR3, CFHR1 | 35 | B/− | Common |
| 11291 | M | 1q31.3 | 196712510 | 144 771 | Loss | CFH, CFHR3, CFHR1, CFHR4 | 80 | D/− | Common |
| 11443 | M | 1q31.3 | 196718380 | 104 459 | Gain | CFHR3, CFHR1 | 88 | B/− | Common |
| 11489 | M | 2q13 | 110852828 | 408 305 | Loss | NPHP1+ 5 genes | 104 | B/+ | Rare |
| 11046 | M | 3p26.1 | 4344934 | 533 721 | Loss | SETMAR, SUMF1, ITPR1, EGOT | 352 | D/+ | Rare |
| 11378 | M | 4q13.2 | 69402972 | 130 793 | Loss | UGT2B17, UGT2B15 | 45 | D/− | Common |
| 11412 | M | 4q13.2 | 69402972 | 126 404 | Loss | UGT2B17, UGT2B15 | 42 | D/− | Common |
| 11338 | M | 5q13.2 | 70193462 | 72 211 | Loss | 5 genes | 16 | D/− | Common |
| 11415 | M | 7q22.1 | 100328032 | 9797 | Gain | ZAN | 34 | B/− | Common |
| 11524 | M | 7q22.1 | 100328032 | 12 551 | Gain | ZAN | 32 | B/− | Common |
| 11345 | M | 11q12.2 | 60965139 | 55 347 | Loss | PGA3, PGA4, PGA5 | 49 | B/− | Common |
| 11499 | M | 11q12.2 | 60965716 | 55 365 | Gain | PGA3, PGA4, PGA5 | 63 | B/− | Common |
| 11197 | M | 12p11.21 | 31267642 | 85 948 | Gain | 0 | 136 | B/− | Common |
| 11303 | M | 12p11.21 | 31277416 | 76 688 | Loss | 0 | 124 | A,B/− | Common |
| 11469 | M | 12p11.21 | 31277416 | 76 368 | Loss | 0 | 142 | B/− | Common |
| 11550 | M | 12p11.21 | 31277416 | 76 368 | Loss | 0 | 120 | B/− | Common |
| 11152 | M | 13q21.1 | 57722436 | 25 162 | Gain | 5 genes | 4 | B/− | Common |
| 11149 | M | 15q11.1 | 20588546 | 45 025 | Loss | 0 | 7 | D/− | Common |
| 11443 | M | 15q11.1-q11.2 | 20588546 | 1 442 028 | Loss | 13 genes | 130 | D/− | Common |
| 11265 | M | 15q11.2 | 22835869 | 600 861 | Loss | 8 genes | 339 | D/+ | Common |
| 11178 | M | 15q13.2 | 30653646 | 35 270 | Loss | CHRFAM7A | 41 | D/− | Common |
| 11178 | M | 15q13.3 | 32445752 | 16 891 | Loss | CHRNA7 | 27 | D/− | Common |
| 11168 | M | 16p13.2 | 8895680 | 317 315 | Gain | PMM2, CARHSP1, USP7, C16orf72 | 240 | D/+ | Rare |
| 11378 | M | 16p11.2 | 32676757 | 618 367 | Gain | TP53TG3, TP53TG3B, LOC653550, SLC6A10P | 21 | B/− | Common |
| 11006 | M | 16q22.1 | 70174866 | 20 901 | Loss | PDPR | 105 | D/− | Common |
| 11327 | M | 16q23.2-q24.1 | 81183435 | 4 772 529 | Loss | 37 genes | 2009 | D/+ | Rare |
| 11353 | F | 17q12 | 34482071 | 2 047 404 | Loss | 27 genes | 1146 | D/+ | Rare |
| 11406 | M | 17q21.31 | 44403033 | 70 700 | Gain | LRRC37A, ARL17B | 6 | B/− | Common |
| 11186 | M | 17q25.3 | 79027376 | 32 869 | Loss | BAIAP2 | 25 | D/+ | Rare |
| 11075 | M | 22q11.1 | 16226253 | 225 102 | Loss | POTEH, OR11H1 | 56 | B/− | Common |
| 11554 | M | 22q11.1 | 16345359 | 89 835 | Loss | 0 | 56 | B/− | Common |
| Inherited autosomal homozygous: 2 common and 1 rare | |||||||||
| 11418 | M | 5q35.3 | 180412358 | 17 430 | Loss | BTNL3 | 23 | A/− | Common |
| 11089 | M | 17q25.3 | 79225034 | 61 | Loss | SLC38A10 | 4 | B,C/− | Rare |
| 11550 | M | 22q13.1 | 39359112 | 26 373 | Loss | APOBEC3A, APOBEC3B | 60 | A,D/− | Common |
| Autosomal complex: 15 common and 2 rare | |||||||||
| 11417 | M | 1q21.3 | 152555599 | 30 626 | Loss | LCE3C | 5 | B/− | Common |
| 11376 | M | 4q13.2 | 69373903 | 117 903 | Gain | UGT2B17 | 15 | B/− | Common |
| 11146 | M | 5q13.2 | 68830681 | 72 261 | Loss | 7 genes | 39 | B/− | Rare |
| 11469 | M | 5q13.2 | 68851539 | 1 518 420 | Loss | 15 genes | 34 | B/− | Rare |
| 11146 | M | 5q13.2 | 70305524 | 83 320 | Loss | 7 genes | 58 | B,D/− | Common |
| 11271 | M | 7q22.1 | 100327877 | 12 750 | Loss | ZAN | 30 | A,B/− | Common |
| 11178 | M | 7q22.1 | 100327877 | 12 750 | Loss | ZAN | 32 | B/− | Common |
| 11076 | M | 7q22.1 | 100328193 | 12 434 | Loss | ZAN | 7 | A,B/− | Common |
| 11152 | M | 14q24.3 | 73994722 | 54 336 | Loss | HEATR4, ACOT1, ACOT2 | 34 | B/− | Common |
| 11156 | M | 14q24.3 | 73994722 | 54 336 | Loss | HEATR4, ACOT1, ACOT2 | 34 | B/− | Common |
| 11197 | M | 14q24.3 | 73994722 | 55 467 | Loss | HEATR4, ACOT1, ACOT2 | 36 | B/− | Common |
| 11353 | F | 14q24.3 | 73994722 | 54 336 | Loss | HEATR4, ACOT1, ACOT2 | 42 | B,D/− | Common |
| 11443 | M | 14q24.3 | 73994722 | 55 467 | Loss | HEATR4, ACOT1, ACOT2 | 34 | B/− | Common |
| 11479 | M | 14q24.3 | 73994722 | 54 336 | Loss | HEATR4, ACOT1, ACOT2 | 34 | B/− | Common |
| 11399 | M | 14q24.3 | 73995172 | 53 886 | Loss | HEATR4, ACOT1, ACOT2 | 38 | A,B/− | Common |
| 11523 | M | 17q21.32 | 45616195 | 54 400 | Gain | NPEPPS | 58 | B/− | Common |
| 11442 | M | 19q13.41 | 52134771 | 13 818 | Loss | SIGLEC14 | 6 | B/− | Common |
| Hemizygous chromosome X: 1 common and 2 rare (all maternal) | |||||||||
| 11411 | M | Xq12 | 67412653 | 21 207 | Loss | OPHN1b | 44 | A/− | Rare |
| 11443 | M | Xq28 | 153857308 | 23 928 | Loss | NCRNA00204B, NCRNA00204, CTAG2 | 13 | D/− | Common |
| 11000 | M | Xq28 | 154770740 | 13 835 | Loss | TMLHE | 5 | B,C/− | Rare |
aValidation test(s) used. A, 1 M Agilent catalog; B, design ID 027305, C, PCR; D, Illumina SNP array. Although not available at the time of submission, we can now report that another analysis of these same samples (17) identified some and not others of the CNVs reported here; /+, reported by Levy et al.; /−, not reported by these authors.
bThe OPHN1 proband call was among the Illumina 1 M SNP array high-confidence parameters; however, the proband's mother DNA did not pass the QC tests.