Table 1.
CNVs detected in patient families with Affymetrix 500K microarrays
| Cytoband |
Estimated size (bp) |
Type |
Status in childrena |
Gene(s) involved |
|---|---|---|---|---|
| Family of Case 1 | ||||
| Proband | ||||
| 3q29 | 2,399,433 | gain | de novo | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 6q16.1 | 60,058 | loss | inherited (paternal)b | no genes; overlaps known CNVs |
| 8p23.1 | 407,187 | gain | inherited (maternal) | FAM86B1, DEFB130, LOC44005; region of segmental duplications and known CNVs |
| Mother | ||||
| 8p23.1 | 202,167 | gain | – | no known genes; numerous cDNAs; region of segmental duplications and known CNVs |
| 10q11.1-q11.21 | 906,591 | gain | – | ZNF33B, BMS1L and numerous cDNAs; region of segmental duplications and known CNVs |
| 11q22.1 | 626,031 | loss | – | cDNA AK128111; overlaps known CNVs |
| 15q11.2 | 1,908,357 | loss | – | OR4N2, OR4M4, POTE15, LOC283755 and multiple cDNAs |
| 22q11.23 | 211,233 | gain | – | LRP5L and multiple cDNAs; region of segmental duplications and known CNVs |
| Father | ||||
| 6q16.1 | 60,058 | loss | – | no genes; overlaps known CNVs |
| 10q11.22 | 124,801 | gain | – | no genes; region of segmental duplications and known CNVs |
| 14q11.2 | 153,147 | gain | – | OR4N2, OR4K2, OR4K5, OR4K1 (odorant receptor gene cluster) |
| Family of Case 2 | ||||
| Mother | ||||
| 3q29 | 2,086,988 | gain | – | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 7q11.23 | 428,467 | gain | – | POMZP3, UPK3B, cDNA BC043544, intron of cDNA BC013192 |
| 14q21.1 | 357,718 | loss | – | cDNA BX248273; encompasses small CNV |
| Proband | ||||
| 3q29 | 2,086,988 | gain | inherited (apparently maternal) | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 7q11.23 | 422,126 | gain | inherited (apparently maternal) | POMZP3, most of UPK3B, cDNA BC043544, intron of cDNA BC013192 |
| 14q11.2 | 219,459 | gain | unknown | OR4Q3, OR4M1, OR4N2, OR4K2, OR4K5, OR4K1 (odorant receptor cluster) |
| 14q21.1 | 368,345 | loss | inherited (maternal)b | cDNA BX248273; encompasses small CNV |
| 15q11.2 | 1,662,281 | gain | unknown | OR4N2, OR4M4, POTE15, LOC283755 and multiple cDNAs |
| 17q21.31 | 183,068 | gain | unknown | 5′ end of KIAA1267, and cDNAs BC018467 and BC000924 |
| Family of Case 3 | ||||
| Proband | ||||
| 3q29 | 1,893,889 | gain | inherited (paternal) | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 8p23.2-p23.1 | 176,963 | gain | inherited (paternal) | 5′ end of MCPH1, and cDNAs including AK025595 |
| 15q11.2 | 1,378,020 | loss | de novoc | OR4N2, OR4M4, POTE15, LOC283755 and multiple cDNAs |
| 19q13.42 | 456,306 | gain | inherited (maternal) | cDNA BX248273; encompasses small CNV |
| Mother | ||||
| 12q24.31 | 114,901 | gain | – | 3′ ends of P2RX7 and CAMKK2, and all of P2RX4 |
| 19q13.42 | 996,692 | gain | – | multiple genes |
| brother 1 | ||||
| 1q31.3 | 142,667 | loss | inherited (paternal)d | CFHR3, CFHR1 and 5′ end of CFHR4 |
| 3q29 | 1,893,889 | gain | inherited (paternal) | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 8p23.2-p23.1 | 221,809 | gain | inherited (paternal) | 5′ end of MCPH1, and cDNAs including AK025595 |
| 10q11.22 | 1,087,629 | gain | inherited (paternal) | GPRIN2, PPYR1, ANXA8L1, ANXA8, and multiple other cDNAs |
| 12q24.31 | 79,614 | gain | inherited (maternal) | 3′ ends of P2RX7 and CAMKK2, all of P2RX4 |
| 14q11.2 | 229,920 | gain | inherited (paternal) | OR4Q3, OR4M1, OR4N2, OR4K2, OR4K5, OR4K1 (odorant receptor gene cluster) |
| 15q11.2 | 1,662,281 | gain | de novoc | OR4N2, OR4M4, POTE15, LOC283755 and multiple cDNAs |
| 19q13.42 | 857,878 | gain | inherited (maternal) | multiple genes |
| Brother 2 | ||||
| 3q29 | 1,893,889 | gain | inherited (paternal) | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 4q24 | 831,405 | gain | inherited (paternal) | TACR3 |
| 8p23.2-p23.1 | 198,636 | gain | inherited (paternal) | 5′ end of MCPH1, and cDNAs including AK025595 |
| 10q11.22 | 848,700 | gain | inherited (paternal) | SYT15, GPRIN2, PPYR1, ANXA8L1 |
| 15q11.2 | 1,662,281 | gain | de novoc | OR4N2, OR4M4, POTE15, LOC283755 and multiple cDNAs |
| 19q13.42 | 541,228 | gain | inherited (maternal) | multiple genes |
| Father | ||||
| 3q29 | 1,893,889 | gain | – | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 4q24 | 556,763 | gain | – | TACR3 |
| 8p23.2-p23.1 | 224,359 | gain | – | 5′ end of MCPH1, and cDNAs including AK025595 |
| 10q11.22 | 848,700 | gain | – | SYT15, GPRIN2, PPYR1, ANXA8L1 |
| 14q11.2 | 222,787 | gain | – | OR4Q3, OR4M1, OR4N2, OR4K2, OR4K5, OR4K1 (odorant receptor gene cluster) |
| Case 4 | ||||
| 2q27.3 | 81,134 | loss | unknown | multiple cDNAs; encompassed by known CNV |
| 3q29 | 2,041,109 | gain | unknown | multiple genes; overlapping with 3q29 microdeletion syndrome (Willatt et al., 2005) |
| 6q24.2-q24.3 | 2,637,073 | gain | unknown | 3′ end of UTRN, EPM2A, GRM1, RAB32, FLJ44955, FBX030, SHPRH, various cDNAs; encompasses several small CNVs |
| 14q11.2 | 249,343 | loss | unknown | OR4N2, OR4K2, OR4K5, OR4K1, OR4K13, OR4K14, OR4K15 (odorant receptor gene cluster; encompasses known CNV and segmental duplications) |
| Xp11.23 | 67,327 | loss | unknown | ZNF630, SSX6; encompasses known CNV and segmental duplications |
a
Parental origin is inferred assuming Mendelian inheritance of CNV events. In Case 2, these are apparently maternal; however, the father's sample was not available for analysis.
b
Parental origin of losses in Case 1 and Case 2 were confirmed by examination of SNP genotypes in these regions.
c
The 15q11.2 region is very complex and apparently de novo events may actually be inherited; in particular, the loss in Case 3 contains multiple heterozygous SNPs and is therefore not a simple hemizygous deletion.
d
SNP genotypes are consistent with paternal inheritance of the 1q31.3 loss in this individual. The corresponding CNV in the father was identified by only one algorithm and thus is not reported.