Skip to main content
. Author manuscript; available in PMC: 2010 May 18.
Published in final edited form as: Nat Genet. 2009 Apr 19;41(5):535–543. doi: 10.1038/ng.367

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
a

This variant introduces a cryptic splice site that causes a truncation.

b

This variant was seen in only two families and generated a lod score of 0.83 in each.

HHS Vulnerability Disclosure