Table 2.
Nineteen rare copy number variants identified in patients with heterotaxy
| ID | Chromosome | Genomic coordinates | Type | Size (kbp) | Genes altered |
|---|---|---|---|---|---|
| 5 | 4q24 | 104,554,264–105,123,728 | Internal dup | 569.464 | TACR3 |
| 5 | 6p22.2 | 26,019,198–26,227,973 | Genic dup | 208.775 | HIST1H3A, HIST1H4A, HIST1H4B, HIST1H3B, HIST1H2AB, HIST1H2BB, HIST1H3C, HIST1H1C, HFE, HIST1H4C, HIST1H1T, HIST1H2BC, HIST1H2AC, HIST1H1E, HIST1H2BD, HIST1H2BE, HIST1H4D, HIST1H3D, HIST1H2AD, HIST1H2BF, HIST1H4E, HIST1H2BG, HIST1H2AE, HIST1H3E |
| 7 | 1q21.1 | 145,625,128–145,927,662 | Genic del | 302.534 | RNF115 , CD160, PDZK1, GPR89A, GPR89C, PDZK1P1 |
| 10 | 5q23.1 | 115,247,380–115,683,172 | Genic dup | 435.792 | AP3S1, AQPEP, LOC644100, COMMD10 |
| 16 | 6p12.1 | 54,138,106–54,277,341 | Genic dup | 139.235 | TINAG |
| 18 | 12p13.33 | 173,786–356,461 | Genic dup | 182.675 | IQSEC3, LOC574538, SLC6A12, SLC6A13 |
| 20 | 12q24.31 | 123,357,010–124,310,519 | Genic dup | 953.509 | VPS37B, ABCB9, OGFOD2, ARL6IP4, PITPNM2, MIR4304, LOC100507091, MPHOSPH9, C12orf65, CDK2AP1, SBNO1, SETD8, RILPL2, SNRNP35, RILPL1, MIR3908, TMED2, DDX55, EIF2B1, GTF2H3, TCTN2 , ATP6V0A2, DNAH10 |
| 20 | 19q13.32 | 47,308,130–47,418,258 | Genic dup | 110.128 | SNAR-E, AP2S1 |
| 26 | 11q12.2 | 60,408,411–60,465,698 | Genic del | 57.287 | LINC00301 |
| 31 | 10p15.1 | 6,254,055–6,374,584 | Internal dup | 120.529 | PFKFB3, LOC399715 |
| 34 | 4q22.2 | 93,875,432–93,988,049 | Genic del | 112.617 | GRID2 |
| 39 | 8q11.1q11.21 | 47,398,661–48,407,568 | Genic dup | 1008.907 | LINC00293, LOC100287846, KIAA0146 |
| 40 | 14q24.2 | 73,620,299–73,786,493 | Genic dup | 166.194 | PSEN1, PAPLN, NUMB |
| 43 | 4q24 | 101,476,709–101,668,938 | Genic del | 192.229 | EMCN-IT3 |
| 59 | 2q24.1 | 157,170,397–157,315,649 | Internal dup | 145.252 | NR4A2, GPD2 |
| 59 | 6q26 | 163,549,870–163,842,358 | Genic dup | 292.488 | PACRG , PACRG-AS1, DKFZp451B082, CAHM, QKI |
| 59 | 9p22.2 | 16,826,417–16,931,236 | Internal dup | 104.819 | BNC2 |
| 63 | 3q25.32 | 158,198,274–158,256,949 | Genic del | 58.675 | RSRC1 |
| 63 | 10q26.3 | 134,358,785–134,921,135 | Genic dup | 562.35 | INPP5A, NKX6–2, TTC40 , LOC399829, GPR123 |
Bold items are candidate genes we identified from rare CNVs
Genic del deletion of at least one coding exon, Genic dup full duplication of at least one gene, Internal dup duplication of internal exons