From: Somatic variants of potential clinical significance in the tumors of BRCA phenocopies
Case # Variant in First Degree Relative | Genea,b | Loc | Variant | Read Depth | Variant Frequencyc | Effect on Proteind | Population Frequencye |
---|---|---|---|---|---|---|---|
1 BRCA2 c.C5645A | PDE4DIP | chr1 | c.4993_4995CG | 1084 | 0.39 | NA | NA |
FOXP1 | chr3 | c.C343G:p.P115A | 487 | 0.26 | 0.996 | 0.0005 | |
PIK3CA a | chr3 | c.A3140G:p.H1047R | 654 | 0.28 | 0.639 | NA | |
APC | chr5 | c.G7450A:p.G2484S | 274 | 0.43 | 0.234 | 0.01 | |
SMO | chr7 | c.C1939T:p.P647S | 65 | 0.72 | 1 | 0.0032 | |
CNTRL | chr9 | c.G5809A:p.E1937K | 349 | 0.44 | 0.841 | 0.0018 | |
TET1 | chr10 | c.C767T:p.A256V | 414 | 0.58 | 0.022 | 0.1 | |
ZMYM2 | chr13 | c.G454C:p.D152H | 441 | 0.28 | 0.997 | 0.0023 | |
ZMYM5 | chr13 | c.A691G:p.T231A | 105 | 0.21 | 0.014 | 0.09 | |
MTUS2 | chr13 | c.C2870T:p.T957 M | 461 | 0.27 | 0.062 | 0.02 | |
2 BRCA1c.IVS17 + 3 A > G | EPHA10 | chr1 | c.C205T:p.R69C | 521 | 0.68 | 1 | 0.0009 |
ETV5 | chr3 | c.C287T:p.S96F | 3463 | 0.52 | 0.999 | NA | |
CSF1R a | chr5 | c.G1237A:p.G413S | 2295 | 0.28 | 0.972 | 0.01 | |
ROS1 | chr6 | c.C3326T:p.S1109 L | 3660 | 0.07 | 0.014 | 0.05 | |
NACA | chr12 | c.A445G:p.K149E | 2927 | 0.38 | 0.999 | 0.07 | |
ZNF668 | chr16 | c.G31A:p.D11N | 3067 | 0.38 | . | NA | |
BRCA1 a | chr17 | c.A926G:p.Q309R | 2105 | 0.06 | 0.999 | 0.03 | |
TP53 a | chr17 | c.A241G:p.K81E | 1475 | 0.11 | 1 | NA | |
3 BRCA2 c.G8107A | ERCC3 | chr2 | c.C2111T:p.S704 L | 59 | 0.29 | 0.642 | 0.0018 |
TET2 | chr4 | c.C86G:p.P29R | 62 | 0.25 | 0.993 | 0.09 | |
PALLD | chr4 | c.A127T:p.T43S | 142 | 0.62 | 0.992 | 0.0005 | |
PDGFRB | chr5 | c.C1223G:p.S408C | 51 | 0.33 | 1 | 0.0005 | |
MLLT4 | chr6 | c.A1264G:p.I422V | 29 | 0.24 | 0.963 | 0.01 | |
ROS1 | chr6 | c.A1611G:p.I537M | 61 | 0.44 | 0.275 | 0.07 | |
KIAA1549 | chr7 | c.G2800A:p.D934N | 30 | 0.47 | 0.89 | 0.03 | |
PTPRD a | chr9 | c.C2983T:p.R995C | 44 | 0.44 | 0.321 | 0.05 | |
NUP98 | chr11 | c.C3424G:p.Q1142E | 38 | 0.54 | 0.359 | 0.06 | |
TRIP11 | chr14 | c.G2134A:p.E712K | 37 | 0.27 | 0.979 | 0.01 | |
MC1R b | chr16 | c.G178 T:p.V60 L | 34 | 0.32 | 0.988 | 0.05 | |
4 BRCA1 c.G5215A | MYOC | chr1 | c.G227A:p.R76K | 1834 | 0.37 | 0.984 | 0.08 |
ROS1 | chr6 | c.G500A:p.R167Q | 2239 | 0.46 | 0.908 | 0.06 | |
FGFR1OP a | chr6 | c.T760C:p.S254P | 1276 | 0.66 | 0.007 | 0.03 | |
FGFR1OP a | chr6 | c.C470T:p.T157I | 2039 | 0.68 | 0.868 | 0.09 | |
FGFR1OP a | chr6 | c.G672 T:p.K224 N | 1821 | 0.70 | 0.001 | 0.09 | |
KIAA1549 | chr7 | c.G2800A:p.D934N | 1214 | 0.47 | 0.89 | 0.03 | |
TRIM24 | chr7 | c.C2514G:p.D838E | 3339 | 0.46 | 0.743 | 0.0027 | |
RET b | chr10 | c.C1946T:p.S649 L | 1054 | 0.44 | 1 | 0.0009 | |
NUP98 | chr11 | c.C3424G:p.Q1142E | 2139 | 0.54 | 0.359 | 0.06 | |
HNF1A | chr12 | c.C293T:p.A98V | 280 | 0.32 | 0.752 | 0.02 | |
MC1R b | chr16 | c.G178 T:p.V60 L | 700 | 0.32 | 0.988 | 0.05 | |
5 BRCA1 c.A2841T | MUC1 | chr1 | c.G586A:p.G196S | 2460 | 0.45 | 0.669 | 0.01 |
PAX3 b | chr2 | c.C941A:p.T314K | 3586 | 0.42 | 0.837 | 0.0041 | |
PAX8 | chr2 | c.T985C:p.F329 L | 2362 | 0.47 | 0.924 | 0.01 | |
HECW1 | chr7 | c.A3692G:p.N1231S | 4508 | 0.46 | 0.998 | 0.0014 | |
WRN | chr8 | c.G340A:p.V114I | 3761 | 0.54 | 0.002 | 0.06 | |
PTPRD a | chr9 | c.C2983T:p.R995C | 3365 | 0.44 | 0.321 | 0.07 | |
NUP98 | chr11 | c.C3424G:p.Q1142E | 3553 | 0.54 | 0.359 | 0.06 | |
CASC5 | chr15 | c.A4339G:p.T1447A | 4457 | 0.40 | 0.336 | 0.05 | |
IGF1R b | chr15 | c.G1532A:p.R511Q | 3795 | 0.43 | 0.476 | 0.0009 | |
CBFA2T3 | chr16 | c.G308C:p.R103P | 2797 | 0.43 | 0.811 | 0.04 | |
SPECC1 | chr17 | c.C579G:p.S193R | 2353 | 0.60 | 1 | 0.1 | |
SSX1 | chrX | c.A149G:p.Y50C | 7574 | 0.46 | 0.97 | 0.0006 | |
6 BRCA1 c.187delAG | FCRL4 | chr1 | c.C34T:p.P12S | 49 | 0.28 | 0.941 | 0.0046 |
MYOC | chr1 | c.G227A:p.R76K | 24 | 0.37 | 0.984 | 0.01 | |
KIAA1549 | chr7 | c.G2800A:p.D934N | 35 | 0.47 | 0.89 | 0.03 | |
LTBP3 | chr11 | c.C1313T:p.A438V | 24 | 0.25 | 0.997 | 0.05 | |
NUP98 | chr11 | c.C3424G:p.Q1142E | 27 | 0.54 | 0.359 | 0.06 | |
BRCA2 b | chr13 | c.A865C:p.N289H | 103 | 0.20 | 0.991 | 0.06 | |
BRCA2 b | chr13 | c.A2971G:p.N991D | 50 | 0.18 | 0 | 0.06 | |
ERCC4 | chr16 | c.G1244A:p.R415Q | 52 | 0.48 | 1 | 0.03 | |
MC1R b | chr16 | c.G178 T:p.V60 L | 17 | 0.32 | 0.988 | 0.05 | |
CHD6 | chr20 | c.C7165T:p.R2389C | 29 | 0.53 | 1 | 0.006 | |
7 BRCA1 c.187delAG | PDE4DIP | chr1 | c.A6002G:p.E2001G | 927 | 0.58 | 0.999 | 0.1 |
PPARG b | chr3 | c.C34G:p.P12A | 923 | 0.46 | 0 | 0.07 | |
ROS1 | chr6 | c.G500A:p.R167Q | 968 | 0.46 | 0.908 | 0.06 | |
ROS1 | chr6 | c.A1611G:p.I537M | 1094 | 0.44 | 0.275 | 0.07 | |
PMS2 b | chr7 | c.G59A:p.R20Q | 877 | 0.45 | 0.924 | 0.07 | |
HNF1A | chr12 | c.C293T:p.A98V | 182 | 0.32 | 0.752 | 0.02 | |
CBFA2T3 | chr16 | c.G308C:p.R103P | 676 | 0.43 | 0.811 | 0.04 | |
8 BRCA1 c.3109insAA | PDE4DIP | chr1 | c.A6002G:p.E2001G | 42 | 0.58 | 0.999 | 0.1 |
FGFR1OP a | chr6 | c.C470T:p.T157I | 29 | 0.69 | 0.868 | 0.03 | |
FGFR1OP a | chr6 | c.T760C:p.S254P | 22 | 0.66 | 0.007 | 0.03 | |
ROS1 | chr6 | c.G500A:p.R167Q | 29 | 0.46 | 0.908 | 0.06 | |
RET b | chr10 | c.C1946T:p.S649 L | 13 | 0.44 | 1 | 0.0009 | |
NUP98 | chr11 | c.G4759A:p.E1587K | 25 | 0.79 | 1 | 0.01 | |
NUP98 | chr11 | c.C3424G:p.Q1142E | 23 | 0.54 | 0.359 | 0.06 | |
BLM | chr15 | c.C2603T:p.P868L | 64 | 0.2 | 0.81 | 0.05 | |
9 BRCA1 c.1793 delA | FANCD2 | chr3 | c.A1634G:p.N545S | 1102 | 0.27 | 0.06 | 0.0046 |
FGFR1OP | chr6 | c.G688C:p.A230P | 1640 | 0.38 | 0.934 | 0.02 | |
ROS1 | chr6 | c.A1611G:p.I537M | 1497 | 0.44 | 0.275 | 0.07 | |
AKAP9 | chr7 | c.G4519C:p.D1507H | 1623 | 0.45 | 0.874 | 0.0005 | |
MYC | chr8 | c.A77G:p.N26S | 838 | 0.56 | 0.977 | 0.02 | |
WRN | chr8 | c.C3236T:p.S1079 L | 1327 | 0.29 | 0.405 | 0.02 | |
CARS | chr11 | c.G38A:p.R13H | 626 | 0.79 | 1 | 0.0032 | |
NUP98 | chr11 | c.G4759A:p.E1587K | 952 | 0.79 | 1 | 0.01 | |
BRCA2 b | chr13 | c.A865C:p.N289H | 1907 | 0.20 | 0.991 | 0.06 | |
BRCA2 b | chr13 | c.A2971G:p.N991D | 1331 | 0.18 | 0 | 0.06 | |
TSC2 b | chr16 | c.G1100A:p.R367Q | 557 | 0.58 | 0.999 | 0.02 | |
ASXL1 | chr20 | c.C3692T:p.S1231F | 1399 | 0.55 | 0.03 | 0.02 | |
CHD6 | chr20 | c.C7165T:p.R2389C | 1628 | 0.53 | 1 | 0.01 | |
10 BRCA2 c.6794 insA | ROS1 | chr6 | c.G500A:p.R167Q | 22 | 0.46 | 0.908 | 0.06 |
NUP98 | chr11 | c.C3424G:p.Q1142E | 10 | 0.54 | 0.359 | 0.06 | |
OMD | chr9 | c.G662A:p.S221 N | 41 | 0.46 | 0 | 0.03 | |
ARNT | chr1 | c.T1506G:p.D502E | 18 | 0.44 | 0.018 | 0.01 | |
PAX3 | chr2 | c.C941A:p.T314K | 14 | 0.42 | 0.837 | 0.02 | |
ARHGEF12 | chr11 | c.A2861T:p.Y954F | 68 | 0.33 | 0.01 | 0.05 | |
PALB2 | chr16 | c.G2993A:p.G998E | 71 | 0.27 | 1 | 0.01 | |
EZH2 | chr7 | c.G436C:p.D146H | 76 | 0.66 | 0.898 | 0.07 | |
11 BRCA2 c.6174 del T | PAX3 b | chr2 | c.C941A:p.T314K | 109 | 0.42 | 0.837 | 0.02 |
PPARG b | chr3 | c.C34G:p.P12A | 49 | 0.46 | 0 | 0.07 | |
PMS2 b | chr7 | c.G59A:p.R20Q | 76 | 0.45 | 0.924 | 0.07 | |
MC1R | chr16 | c.G178 T:p.V60 L | 34 | 0.32 | 0.988 | 0.05 | |
MYOC | chr1 | c.G227A:p.R76K | 84 | 0.37 | 0.984 | 0.08 | |
PTPRD a | chr9 | c.C2983T:p.R995C | 44 | 0.44 | 0.321 | 0.07 | |
SSX1 | chrX | c.A149G:p.Y50C | 192 | 0.46 | 0.97 | 0.0006 | |
MUC1 | chr1 | c.G586A:p.G196S | 110 | 0.45 | 0.669 | 0.01 | |
FANCD2 | chr3 | c.G521A:p.R174Q | 34 | 0.21 | 0.96 | 0 | |
CNTRL | chr9 | c.C6221A:p.A2074D | 34 | 0.83 | 0.8 | 0.0041 | |
PDE4DIP | chr1 | c.G2838A:p.M946I | 25 | 0.59 | 0.028 | 0.09 | |
PDE4DIP | chr1 | c.G4111A:p.V1371I | 78 | 0.24 | 0.012 | 0.07 |