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. 2016 Mar;2(2):a000620. doi: 10.1101/mcs.a000620

Table 1.

Genomic variants detected by whole-exome sequencing

Gene symbol Chromo-some HGVS DNA reference HGVS protein reference Variant type dbSNP/COSMIC ID Comment Pre-tx depth Pre-tx allelic ratio Post-tx depth Post-tx allelic ratio Normal depth Normal allelic ratio
FUBP1 Chr1 g.chr1:78422351C>T p.W537* Stop Gained n/a Pre-tx only 107 0.26 132 0 61 0
RNF212 Chr4 g.chr4:1079732A>G p.L105S Missense n/a Pre-tx only 99 0.32 153 0 94 0
RP1 Chr8 g.chr8:55541441TC>T p.S1667fs Frameshift n/a Pre-tx only 125 0.04 267 0 163 0
CPXM2 Chr10 g.chr10:125622146C>T p.G166E Missense n/a Pre-tx only 39 0.08 53 0 49 0
CACNA1C Chr12 g.chr12:2788661C>T p.R1704W Missense rs373996684 Pre-tx only 184 0.18 322 0 175 0
ABCC9 Chr12 g.chr12:22005137C>A p.G888V Missense n/a Pre-tx only 72 0.18 182 0 102 0
NTS Chr12 g.chr12:86272172G>A p.C62Y Missense n/a Pre-tx only 89 0.15 266 0 108 0
CACNA1H Chr16 g.chr16:1252074G>A p.E542K Missense n/a Pre-tx only 58 0.07 158 0 35 0
AMFR Chr16 g.chr16:56396967G>A p.R596C Missense n/a Pre-tx only 33 0.09 29 0 28 0
SPEN Chr1 g.chr1:16259731CCAGAAAACAACCCGAT>C p.QKTTRS2333fs Frameshift n/a Both 138 0.35 184 0.66 122 0
SYT6 Chr1 g.chr1:114640393C>T p.A406T Missense rs142164979 Both 61 0.23 83 0.29 42 0
ZDBF2 Chr2 g.chr2:207175047G>A p.R1932H Missense COSM2150473 Both 173 0.21 209 0.42 145 0
YEATS2 Chr3 g.chr3:183515744C>T p.P1044L Missense rs376025260 Both 70 0.21 115 0.30 58 0
CCDC71L Chr7 g.chr7:106300865T>G p.S160R Missense n/a Both 13 0.23 17 0.35 15 0
KIAA1045 Chr9 g.chr9:34971537G>A p.R81Q Missense rs374394658 Both 139 0.18 173 0.39 97 0
CCDC180 Chr9 g.chr9:100092618C>G p.P659A Missense n/a Both 107 0.26 148 0.38 93 0
CNNM1 Chr10 g.chr10:101090101G>C p.E319D Missense n/a Both 158 0.15 189 0.35 132 0
MICAL2 Chr11 g.chr11:12278507A>G p.D1044G Missense n/a Both 34 0.29 50 0.36 23 0
KDM4E Chr11 g.chr11:94760214A>G p.N498S Missense n/a Both 69 0.13 63 0.33 35 0
TSPAN8 Chr12 g.chr12:71526521A>T p.D176E Missense n/a Both 182 0.18 287 0.37 180 0
CORO6 Chr17 g.chr17:27942821C>T p.V450M Missense n/a Both 122 0.25 171 0.32 92 0
AKAP1 Chr17 g.chr17:55183750AGCTTGGATAGAAATGAGGAGG>A p.SLDRNEEG309S Codon Deletion COSM1244721 Both 151 0.11 181 0.06 84 0
NOTCH3 Chr19 g.chr19:15280935A>T p.W1721R Missense n/a Both 12 0.50 12 0.25 10 0
CPAMD8 Chr19 g.chr19:17017774C>T p.A1386T Missense n/a Both 148 0.23 159 0.37 104 0
ZNF420 Chr19 g.chr19:37618255A>G p.N121S Missense n/a Both 99 0.21 244 0.35 134 0
ZNF473 Chr19 g.chr19:50550059A>T p.R787* Stop Gained n/a Both 180 0.26 205 0.36 135 0
KRTAP10-3 Chr21 g.chr21:45978592T>C p.T3A Missense rs452472 Both 13 0.62 7 0.43 0 0
HTRA2 Chr2 g.chr2:74757932T>A p.L232Q Missense n/a Post-tx only 256 0.00 225 0.23 103 0
LRAT Chr4 g.chr4:155665556T>A p.S26R Missense n/a Post-tx only 352 0 235 0.03 169 0
CREB3 Chr9 g.chr9:35736430T>G p.Y275D Missense n/a Post-tx only 87 0 81 0.07 68 0
ALOX5 Chr10 g.chr10:45907697T>G p.L164V Missense n/a Post-tx only 280 0 219 0.05 133 0
KNDC1 Chr10 g.chr10:135013889G>T p.E972* Stop Gained n/a Post-tx only 87 0 62 0.15 45 0
SLITRK6 Chr13 g.chr13:86368728T>TA p.Y639Lfs Frameshift n/a Post-tx only 278 0 762 0.14 175 0
PML Chr15 g.chr15:74336964G>C p.R755P Missense n/a Post-tx only 471 0 363 0.07 235 0
ARHGAP35 Chr19 g.chr19:47423891GC>AA p.P654T Missense n/a Post-tx only 217 0 179 0.13 109 0
RRP1 Chr21 g.chr21:45213265C>T p.R114C Missense n/a Post-tx only 196 0 136 0.14 83 0

HGVS, Human Genome Variation Society; dbSNP, Database of Single Nucleotide Polymorphisms; COSMIC, Catalogue of Somatic Mutations in Cancer; Pre-tx, pretreatment sample; Post-tx, postprogression sample; n/a, not applicable.