Table 3.
Truncating and read-through variants identified in the screen
Region of X chrom |
Gene | Family number |
LOD | Truncating variants in cases |
Stop position |
Protein size (aa) |
Truncating variants in controls |
Frequency in controls |
Mutations in known MR genes |
Abnormal transcript identified |
Ref. | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Truncating | ||||||||||||
Recurrent | X specific | MAGEE2 | – | – | 358G>T, E120* | 120 | 524 | 358G>T, E120* | 4/244 | |||
X specific | UBE2NL | – | – | 266T>G, L89* | 89 | 154 | 266T>G, L89* | 100/283 | ||||
PAR | GTPBP6 | – | – | 118C>T, Q40* | 40 | 287 | 118C>T, Q40* | 117/243 | ||||
Nonrecurrent (>1 variant/gene) | X specific | AP1S2 | 445 | 3.85 | 106C>T, Q36* | 36 | 157 | 0/726 | 16 | |||
502 | 2.36 | 154C>T, R52* | 52 | 157 | 0/726 | 16 | ||||||
63 | 2.2 | IVS 3–2 delTACA | 64 | 157 | 0/726 | 16 | ||||||
X specific | BRWD3 | 322 | 0.03 | IVS 29 +1 G>T | 1,093 | 1,802 | 0/520 | Yes | 20 | |||
336 | 0.26 | 946_947insA, R316fs*22 | 337 | 1,802 | 0/520 | 20 | ||||||
X specific | CUL4B | 42 | 0.58 | 1007_1011delTTATA, I336fs*2 | 338 | 913 | 0/637 | 17 | ||||
307 | 0.88 | 1162C>T, R388* | 388 | 913 | 0/637 | 17 | ||||||
43 | 2.93 | 2566C>T, R856* | 856 | 913 | 0/637 | 17 | ||||||
329 | 0.59 | IVS 7–2 A>G | 308 | 913 | 0/637 | Yes | 17 | |||||
363 | 0.42 | 2493G>A, T831Ta | 806 | 913 | 0/637 | Yes | 17 | |||||
X specific | ITIH5L | 32 | −1.38 | 670C>T, R224* | 224 | 1,313 | 0/489 | IL1RAPL1 | ||||
74 | −0.63 | IVS 7 +1 ins T | 1,313 | IVS 7 +1 ins T | 1/528 | |||||||
X specific | SLC9A6 | 197 | 1.79 | 1402C>T, R468* | 468 | 669 | 0/282 | 21 | ||||
227 | 0.87 | 51 1_512delAT | 230 | 669 | 0/282 | 21 | ||||||
X specific | UPF3B | 407 | −0.55 | 674_677delGAAA, R225fs*22 | 275 | 483 | 0/730 | 18 | ||||
309 | 0.56 | 867_868delAG, G290fs*2 | 292 | 483 | 0/730 | 18 | ||||||
62 | 2.66 | 1288C>T, R430* | 430 | 483 | 0/730 | 18 | ||||||
X specific | ZDHHC9 | 152 | 0.23 | 175_176insCGCT, Y59fs*33 | 92 | 364 | 0/445 | 19 | ||||
602 | 0.49 | IVS 3 +5 G>C | 43 | 364 | 0/445 | Yes | 19 | |||||
Nonrecurrent (1 variant/gene) | X specific | ARSF | 263 | 0.26 | IVS 8 +5 G>A | 591 | 0/217 | |||||
X specific | ATXN3L | 324 | −1.47 | 76G>T, 26 * | 26 | 355 | 76G>T, E26* | 1/336 | ||||
X specific | BEX4 | 232 | 1.03 | IVS 1 +1 G>A | 447 | IVS 1 +1 G>A | 2/530 | |||||
X specific | DRP2 | 306 | −3.76 | IVS 10 +1 G>C | 372 | 957 | 0/247 | Yes | ||||
X specific | FAM47B | 241 | 0.66 | 331C>T, Q111* | 111 | 645 | 0/233 | MECP2 | ||||
X specific | MAP3K15 | 430 | −1.11 | 1069C>T, R357* | 357 | 788 | 1831C>T, R611* | 2/272 | ||||
1789C>T, R597* | 1/243 | |||||||||||
X specific | MAP7D3 | 141 | −1.05 | IVS 9 +1 G>C | 567 | 877 | 0/460 | Yes | ||||
X specific | P2RY4 | 400 | 0.26 | 1043G>A, W348* | 348 | 366 | 303G>A, W101* | 3/249 | ||||
X specific | RPL9P7 | 116 | −0.71 | 75delT, I26fs*2 | 27 | 192 | 0/266 | |||||
X specific | SAGE1 | 32 | 0.88 | 621T>A, C207* | 207 | 904 | 0/273 | IL1RAPL1 | ||||
X specific | SATL1 | 197 | −6.46 | 1325G>A, W442* | 442 | 632 | 0/284 | SLC9A6 | ||||
X specific | SSX6 | 81 | −0.03 | 111G>A, W37* | 37 | 188 | 0/274 | |||||
X specific | SYP | 346 | 0.49 | 274_275insA, T92fs*45 | 137 | 313 | 0/272 | |||||
X specific | SYTL5 | 438 | −0.51 | 1633G>T, G545* | 545 | 730 | 0/464 | |||||
X specific | USP9X | 383 | 1.18 | 7505delA, Q2502fs*18 | 2,520 | 2,547 | 0/282 | |||||
X specific | VSIG4 | 468 | 0.00 | 973A>T, R325* | 325 | 399 | 0/524 | |||||
X specific | ZCCHC13 | 267 | −1.37 | 45G>A, W15* | 15 | 168 | 0/263 | |||||
X specific | ZNF183 | 581 | 1.20 | 901C>T, Q301* | 301 | 343 | 0/252 | |||||
X specific | ZNF711 | 208 | 1.31 | 2157_2158delTG, 719fs*1 | 720 | 771 | 0/252 | |||||
PAR | IL9R | 432 | – | 58C>T, R20* | 20 | 522 | 0/248 | |||||
Read-through | ||||||||||||
Recurrent | PAR | ASMTL | – | – | 1864delT, *622fs*8 | 630 | 622 | 1864delT, *622fs*8 | 71/223 | |||
X specific | H2BFWT | – | – | 510delA, Q171fs*30b | 201 | 175 | 0/260 | |||||
Nonrecurrent | X specific | NSDHL | 577 | 1.06 | 1098_1099insT, R367fs*31 | 398 | 374 | 0/224 | ||||
X specific | CXorf12 | 340 | 0.26 | 782delG, R261fs*11 | 272 | 262 | 0/293 | MECP2 |
This variant introduces a cryptic splice site that causes a truncation.
This variant was seen in only two families and generated a lod score of 0.83 in each.