Table 2.
SNVs on chromosome X that change the protein coding region in PEL
| Gene | AA | Change | Frequency* | mRNA† | Name |
| DHRSX | 292, 247 | His > Arg, Val > Leu | 8/8 | nd | Dehydrogenase/reductase (SDR family) |
| ARHGAP6 | 202, 200 | Asn > Lys, Thr > Pro | 8/8 | No | Rho GTPase-activating protein 6 |
| RAI2 | 202 | Met > Val | 8/8 | No | Retinoic acid-induced protein 2 |
| MAGEB2 | 61 | Glu > Lys | 8/8 | Yes | Melanoma-associated antigen B2 |
| TAB3 | 394 | Trp > Arg | 8/8 | nd | TGF-β-activated kinase 1 |
| DMD | 477 | Arg > Gln | 8/8 | Yes | Dystrophin Dp71ab isoform |
| RPGR | 889,887,878,880 | Glu > Gly | 8/8 | Yes | Retinitis pigmentosa GTPase regulator |
| SSX5 | 19 | Glu > Gln | 8/8 | Yes | Synovial sarcoma, X breakpoint 5 |
| WDR13 | 325 | His > Arg | 8/8 | Yes | WD repeat-containing protein 13 |
| CCDC120 | 571 | Ala > Gly | 8/8 | nd | Coiled-coil domain containing protein 120 |
| MAGIX | 112,45‡ | His > Arg | 8/8 | No | PDZ domain-containing protein MAGIX |
| 173,97 | Phe > Leu | ||||
| 323,247,242 | Val > Leu | ||||
| FAM120C | 1083, 1082 | Gln > Pro, Ile > Thr¶ | 8/8 | Yes | Family with sequence similarity 120C |
| MTRNR2L10 | 3,2 | Thr > Pro, Ala | 8/8 | nd | Humanin-like protein 10 |
| ZXDB | 764 | Asp > Asn | 8/8 | nd | Zinc finger X-linked protein ZXDB |
| EDA2R | 129 | Thr > Ala | 8/8 | No | Ectodysplasin A2 receptor |
| ATP7A | 1350 | Glu > Lys | 8/8 | Yes | Copper-transporting ATPase |
| POU3F4 | 237 | Gly > Ala | 16/16 | Yes | POU domain, class 3, factor 4 |
| RNF128 | 135 | Phe > Tyr | 8/8 | No | E3 ubiquitin-protein ligase RNF128 |
| GUCY2F | 296 | Arg > Gln | 8/8 | No | Retinal guanylyl cyclase 2 |
| LRCH2 | 398 | Asp > Asn | 8/8 | nd | Leucine-rich repeat and calponin homology domain-containing protein 2 |
| 723 | Arg > Cys | ||||
| BCORL1 | 111, 660 | Phe > Leu, Val > Gly | 16/16 | Yes | BCL6 corepressor-like protein 1 |
| RAB33A | 35 | Arg > Gly | 8/8 | Yes | Ras-related protein Rab-33A |
| DDX26B | 843 | Ile > Gly | 8/8 | nd | DEAD/H (Asp-Glu-Ala-Asp/His) box |
| ATP11C | 114 | Cys > Trp | 8/8 | nd | ATP11C ATPase, class VI, type 11C |
| MAGEC1 | 102, 103 | Ser > Pro/Cys, P > S | 8/8 | Yes | Melanoma-associated antigen C1 |
| CXorf40A | 70 | Thr > Ala | 8/8 | Yes | Chromosome X orf40 A |
| MAGEA10 | 234, 166 | Val > Ile, Arg > Lys | 8/8 | Yes | Melanoma-associated antigen 10 |
| SLC6A8 | 431,421,316 | Asp > Asn | 16/16 | No | Sodium- and chloride-dependent creatine transporter 1 |
| 454,444,339 | Cys > Arg | ||||
| 504,494,389 | Met > Thr | ||||
| 590,580,475 | Arg > Cys | ||||
| 592,582,477 | Gln > Lys | ||||
| 636,626,521 | STOP > Gly | ||||
| ABCD1 | 606 | Ser > Pro | 16/16 | Yes | ATP-binding cassette subfamily D member 1 |
| 635, 712 | Val > Met, Arg > His | ||||
| PLXNB3 | 1156, 1535 | Glu > Asp, Met > Thr | 8/8 | No | Plexin-B3 |
| IRAK1 | 196 | Phe > Ser | 8/8 | Yes | Interleukin 1 receptor kinase 1 |
| VBP1 | 123 | Met > Val | 8/8 | Yes | Prefoldin subunit 3 |
| TCEAL6 | 175 insC | Gln > fs | 8/8 | nd | Transcription elongation factor A-like 6 |
| TEX13A | 201 ins,199 ins | Trp > fs, Gly > fs | 8/8 | No | Testis-expressed 13A |
nd, not determined.
*
Number of mutant samples/number of samples with coverage ≥30× (frequency), additional samples had <30× coverage, and even though they often had the same mutation on confirmatory sequencing, we did not include them here.
†
Based on GEO data sets GSE2149 and GDS1063.
‡
More than one amino acid position resulting from differential splicing, which generates isoforms.
¶
Low coverage.