Table 1.
Subjects and SPAST CNVs
| Subject | Del versus Dup | SPAST Exon(s) Affected (of 17) | Other Genes Deleted or Duplicated | CNV Size (kb) | Spastic Paraplegia | Origin | Novel Rearrangementa | Notes |
|---|---|---|---|---|---|---|---|---|
| A1 | del | 17 | – | 5.5 | y | USA | – | |
| A2 | del | 17 | – | 14.4 | y | USA | – | complex |
| A3 | del | 17 | SLC30A6 ex 1–5 (of 15) | 24.6 | y | USA | – | |
| A4 | del | 17 (partial) | – | 2.7 | y | USA | y | |
| A5 | del | 17 | SLC30A6 ex 1–2 (of 15) | 18.4 | y | USA | – | |
| A6 | del | 17 | SLC30A6 ex 1–2 (of 15) | 25.7 | y | USA | – | |
| A8 | del | 17 (partial) | – | 2.7 | y | USA | y | |
| A9 | del | 17 (partial) | – | 2.7 | y | USA | y | |
| A10 | dup | 13–15 | – | 6.2 | y | USA | y | tandem, directly oriented duplication |
| BAB 3166 | del | 13 | – | 1.3 | n (at age 16) | USA | NA | reported in Boone et al.26 |
| BAB 5112 | del | 5–17 | SLC30A6, NLRC4, YIPF4, BIRC6, MIR558, MIR4765, and TTC27 ex 1–5 (of 20) | 559.3 | y | USA | y | |
| BAB 3200 | del | 1–7 | DPY30 ex 1–3 (of 5) | 87.2 | y | USA | NA | complex; reported in de Ligt et al.27 |
| BAB 3327 | del | 17 | – | 5.5 | y | USA | – | |
| SPAST_1 | del | 17 (partial) | – | 2.7 | ?b | USA | y | |
| SPAST_3 | dup | 2–17 | SLC30A6, NLRC4, YIPF4, and BIRC6 ex 1–46 (of 74) | 432.2 | ?b | USA | y | tandem, directly oriented duplication |
| Spain 1 | del | 5–16 | – | 43.4 | y | Spain | y | |
| Spain 2 | del | 13–17 | SLC30A6, NLRC4, YIPF4, MIR558, and BIRC6 ex 1–66 (of 74) | 455.0 | y | Spain | y | |
| Spain 3 | del | 3–17 | SLC30A6 ex 1–5 (of 15) | 95.7 | y | Spain | – | |
| Spain 4 | del | 8–17 | SLC30A6 ex 1–5 (of 15) | 60.7 | y | Spain | – | |
| Spain 5 | del | 1 | – | 12.6 | y | Spain | – | |
| Spain 6 | del | 2–17 | SLC30A6 and NLRC4 ex 5–9 (of 9) | 170.1 | y | Spain | – | |
| Spain 7 | del | 10–16 | – | 16.0 | y | Spain | – | |
| Spain 8 | del | 2–7 | – | 48.9 | y | Spain | y | |
| Spain 9 | del | 6–7 | – | 5.0 | y | Spain | – | |
| JKF B | del | 16 | – | 2.0 | y | USA | – | |
| JKF C | dup | 9 | – | 6.7 | y | USA | y | tandem, directly oriented duplication |
| Ruhr 3 | del | 2–9 | – | 65.4 | y | Germany | – | |
| Ruhr 4 | del | 1 | – | 20.5 | y | Germany | – | |
| Ruhr 5 | del | 2–9 | – | 65.4 | y | Germany | – | |
| Ruhr 6 | del | 5–6 | – | 8.3 | y | Germany | – | |
| Ruhr 7 | del | 17 (partial) | – | 5.1 | y | Germany | y | |
| Ruhr 9 | del | 1 | – | 4.0 | y | Germany | – | |
| Ruhr 10 | del | 1 | – | 4.0 | y | Germany | – | |
| Ruhr 11 | del | 2–7 | – | 33.5 | y | Germany | y | |
| Ruhr 12 | del | 1 | – | 16.3 | y | Germany | – | |
| Ruhr 13 | del | 8–17 | SLC30A6 ex 1 (of 15) | 44.8 | y | Germany | – | |
| Ruhr 14 | del | 16–17 | SLC30A6 ex 1–4 (of 15) | 31.7 | y | Germany | – | |
| Ruhr 15 | del | 2–12 | – | 72.9 | y | Germany | y | |
| Ruhr 16 | del | 5 | – | 1.9 | y | Germany | – | |
| Ruhr 17 | del | 9–17 (partial) | – | 27.5 | y | Germany | y | |
| Ruhr 18 | del | 8–17 | SLC30A6 ex 1 (of 15) | 44.8 | y | Germany | – | |
| Ruhr 21 | del | 10–17 (partial) | – | 20.9 | y | Germany | y | |
| Ruhr 23 | del | 17 | – | 17.6 | y | Germany | – | |
| Ruhr 26 | del | 13–16 | – | 7.3c | y | Germany | – | |
| Ruhr 27 | del | 17 | SLC30A6 ex 1–2 (of 15) | 24.1 | y | Germany | – | complex |
| Ruhr 28 | del | 1 (partial) | – | 16.5 | y | Germany | – | |
| Ruhr 29 | del | 8–17 | SLC30A6, NLRC4, YIPF4, BIRC6, MIR558, MIR4765, TTC27, LINC00486, LOC100271832, LTBP1, 5S_rRNA | 1,283.9 | y | Germany | – | |
| Ruhr 31 | del | 8–9 | – | 9.3 | y | Germany | – | |
| Ruhr 32 | del | 2–13 | – | 59.4c | y | Germany | y | |
| Park 1 | del | 5–7 | – | 11.7 | y | Korea | – | |
| Park 2 | del | 5 (partial)–7 | – | 8.1 | y | Korea | y | |
| Park 3 | del | 8–9 | – | 8.9 | y | Korea | – | |
| Park 4 | del | 4–17 | SLC30A6 ex 1–9 (of 15) | 100.5 | y | Korea | – | |
| A37 | del | 17 | – | 10.8 | y | USA | NA | reported in Boone et al.14 |
| A38 | del | 17 | – | 16.8 | y | USA | NA | complex; reported in Boone et al.14 |
| A39 | del | 17 | – | 5.5 | y | USA | NA | reported in Boone et al.14 |
| Iwanaga | del | 1 (partial) | – | 2.3 | y | Japan | NA | reported in Iwanaga et al.28 |
| Mitne-Neto | dup | 10–12 | – | 4.0 | y | Brazil | NA | reported in Mitne-Neto et al.11; tandem, directly oriented duplication |
| Miura | del | 1–4 | DPY30 ex 1–3 (of 5) | 69.8 | y | Japan | NA | reported in Miura et al.40 |
Abbreviations are as follows: ex, exon; y, yes; n, no; NA, not applicable; –, no or none.
a
Based on SPAST exon or combination of exons rearranged and ploidy (del versus dup). Rearrangement of part of an exon is considered to be distinct from rearrangement of the whole exon. Previously published CNVs derived from Loureiro et al.,5 Álvarez et al.,9 Boone et al.14,26 Sulek et al.,41 and Myers et al.42
b
Phenotype unknown.
c
CNV breakpoint could not be sequenced. CNV length is an average of the minimum and maximum CNV interval identified by aCGH.