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Table 2 Mutations in BC associated genes detected by NGS in a series of 45 Lebanese patients

From: Next-generation sequencing in familial breast cancer patients from Lebanon

Family number/Patient code Genes Results HGMD Professional ExAC allele frequency
1/B19 XRCC3 c.C722T p.T241M DFP Association with melanoma 0.3075
XRCC1 c.G839A p.R280H DFP Association with increased lung cancer 0.08811
CASP8 c.*429A > G Not found Not found
BRCA2 c.C65T p.A22V Not found Not found
MUTYH c.C1258G p.L420V Not found Not found
SLX4 c.C1837T p.Q613X Not found Not found
2/B21 BRCA1 c.A536G p.Y179C DM Breast and/or ovarian cancer 0.0002718
ATM c.T2572C p.F858L DP Association with breast cancer 0.009149
ATM c.C3161G p.P1054R DFP Association with breast cancer 0.01692
TP53 c.C215G p.P72R DFP Association with Lung cancer 0.6600
3/B22 BRCA2 c.C5744T p.T1915M DP Association with breast cancer risk 0.01790
ARL11 c.G446A p.W149X DP Association with cancer 0.009898
TP53 c.C215G p.P72R DFP Association with Lung cancer 0.6600
ERCC3 c.C508T p.R170X Not found Not found
VHL c.A631C p.M211L Not found 0.00004623
MRE11A c.C1491T p.I497I Not found 0.0006514
PTCH1 c.G4054A p.V1352I Not found Not found
4/B23 TP53 c.C215G p.P72R DFP Association with Lung cancer 0.6600
TP53 c.C245T p.P82L DM Breast cancer 0.00001657
BRCA2 c.A1114C p.N372H DFP Association with Breast cancer 0.2779
FANCA c.G1038C p.W346C Not found 0.00006621
POLE c.C3890T p.S1297L Not found 0.00002580
POLD1 c.T2257C p.Y753H Not found Not found
GATA2 c.C1040T p.T347I Not found Not found
5/B24 BRCA2 c.G8775C p.Q2925H Not found 0.000008322
APC c.C6821T p.A2274V DM Adenomatous polyposis coli 0.0009917
EZH2 c.C349T p.Q117X Not found Not found
6/B25 XRCC3 c.C722T p.T241M DFP Association with melanoma 0.3075
MLH1 c.A655G p.I219V DP Colorectal cancer, non-polyposis 0.2325
RAD51D c.G494A p.R165Q Not found Not found
ATM c.496 + 4 T > C Not found 0.00009891
PPM1D c.G275C p.C92S Not found Not found
STK11 c.375-1C > T DM Colorectal cancer Not found
7/B26 XRCC3 c.C722T p.T241M DFP Association with melanoma 0.3075
MSH2 c.C1045G p.P349A DM Renal cell carcinoma 0.00009062
MUTYH c.C1174A p.L392M Not found Not found
MUTYH c.C1258A p.L420M DM? Colorectal cancer Not found
ATM c.496 + 4 T > C Not found 0.00009891
RB1 c.C1505T p.T502I Not found 0.00001098
PPM1D c.G275C p.C92S Not found Not found
8/B27 XRCC3 c.C722T p.T241M DFP Association with melanoma 0.3075
BRCA1 c.A1067G p.Q356R DP Association with breast and/or ovarian cancer 0.04407
XRCC1 c.C580T p.R194W DFP Benign breast disease 0.09276
CDH1 c.G1774A p.A592T DM? Breast cancer 0.003212
35/B28 BARD1 c.1071_1091del p.357_364del Not found Not found
ABCC12 c.G490T p.G164X DM Bladder cancer 0.003185
MCC c.G152T p.G51V Not found 0.0001346
9/B31 ATM c.T2119C p.S707P DFP Association with Breast cancer 0.007927
FANCA c.C4232T p.P1411L Not found 0.0001318
36/B32 ATM c.C2770T p.R924W Not found 0.00004942
ALK c.T4211C p.L1404P Not found 0.00008370
10/B33 BRIP1 c.A3571G p.I1191V Not found 0.00004967
NSD1 c.2224_2243del p.P742fs Not found Not found
FANCG c.G1298C p.R433P Not found 0.00004118
FLCN c.T1387C p.Y463H Not found 0.00003298
PTCH1 c.A3749G p.Y1250C Not found Not found
11/B34 XRCC4 c.T401C p.I134T DP Association with Lung cancer 0.02505
RAD51C c.G376A p.A126T FP Reduced activity 0.003529
12/B35 ARL11 c.G571A p.G191R Not found 0.00002188
Rad50 c.A280C p.I94L DM? Breast and/or ovarian cancer 0.003473
POLE c.G2276A p.R759H Not found 0.00001647
13/B36 BRCA1 c.G131T p.C44F DM Breast and/or ovarian cancer Not found
SLX4 c.G421T p.G141W DM Breast and/or ovarian cancer 0.0008237
STK11 c.C1211T p.S404F DM Peutz-Jeghers syndrome 0.0009281
PALB2 c.G2993A p.G998E DP Breast cancer, increased risk- 0.01579
BRCA2 c.C1151T p.S384F DM? Breast cancer 0.0006789
DICER1 c.A5276G p.K1759R Not found 0.00004942
CEBPA c.T122C p.I41T Not found Not found
RECQL4 c.G3314A p.G1105D Not found 0.005430
14/B37 RAD50 c.G379A p.V127I Not found 0.001653
CASP8 c.A1117G p.I373V Not found Not found
RECQL4 c.C3184T p.R1062W Not found 0.0003129
WRN c.G4129A p.G1377S Not found 0.00002483
15/B38 BARD1 c.C119T p.A40V Not found 0.00004775
PTCH1 c.169_170delCT p.57_57del Not found 0.000008913
PTCH1 c.A3749G p.Y1250C Not found Not found
PTCH1 c.C4126T p.R1376W Not found Not found
ERCC5 c.A1904G p.H635R Not found Not found
DICER1 c.C3811T p.L1271F Not found Not found
16/B39 CDKN2A c.G442A p.A148T DP Association with melanoma 0.02278
RAD51D c.A758G p.E253G Not found 0.01144
ERCC6 c.C2800A p.P934T DM Cockayne syndrome Not found
17/B40 MSH2 c.A1787G p.N596S DM Colorectal cancer, non-polyposis 0.0002558
ATM c.A1982C p.D661A Not found Not found
PMS2 c.G1688T p.R563L DM? Colorectal cancer, non-polyposis 0.005813
GPC3 c.78_79insCCG p.P27delinsPP Not found Not found
18/B41 BRCA2 c.658_659delGT p.V220I* DM Breast and/or ovarian cancer 0.00006119
SLX4 c.G3337C p.G1113R Not found 0.000008237
SMARCA4 c.C1098G p.I366M Not found 0.00002715
EPHX1 c.G1040C p.R347T Not found 0.00003296
19/B42 wwoxtv2 c.A544G p.K182E DM? cancer Not found
ATM c.A5558T p.D1853V DP Association with breast cancer, contralateral 0.005186
RET c.C2508T p.S836S DP Association with thyroid cancer 0.04666
BRCA1 c.5090_5093delGTTA p.L1697fs Not found Not found
20/B43 PALB2 c.G2014C p.E672Q DM? Breast cancer? (common variant) 0.02239
PALB2 c.G2993A p.G998E DP Breast cancer (common variant) 0.01579
RAD51C c.G376A p.A126T FP Reduced activity 0.003529
Tp53 c.673-36G > C DFP Breast cancer Not found
21/B44 SLX4 c.G421T p.G141W DM Breast and/or ovarian cancer 0.0008237
SLX4 c.C1919A p.T640N Not found Not found
FANCM c.A5224G p.I1742V Not found 0.008398
POLD1 c.G2793C p.K931N Not found Not found
22/B45 ATM c.A5071C p.S1691R DM Ataxia telangiectasia 0.002019
BRIP1 c.G2220T p.Q740H DM? Breast and/or ovarian cancer 0.0004614
RET c.C2508T p.S836S DP Association with thyroid cancer 0.04666
FANCA c.A796G p.T266A DP Associated with breast cancer 0.5166
23/B46 BARD1 c.1071_1091del p.357_364del Not found Not found
FANCA c.C3412G p.L1138V Not found 0.001533
MRE11A c.A1728T p.R576R Not found 0.000008238
SLX4 c.C1186G p.L396V Not found Not found
37/B47 SLX4 c.A5501G p.N1834S Not found 0.005542
ERCC4 c.G1633C p.G545R Not found 0.000008243
38/B48 SDHC c.C31T p.R11C Not found 0.000008252
FANCD2 c.A1348G p.I450V Not found 0.0003871
FANCF c.C959T p.P320L Not found 0.01264
TSC2 c.A2834G p.K945R Not found Not found
DIS3L2 c.1651_1652insGGG p.A551delinsGA Not found Not found
GNAS c.C1046T p.P349L Not found Not found
24/B49 BRCA1 c.C4327T p.R1443* DM Breast cancer Not found
MSH2 c.C1045G p.P349A DM Renal cell carcinoma 0.00009062
MSH2 c.G965A p.G322D DM? Colorectal cancer, non-polyposis 0.01411
BARD1 c.G253T p.V85L Not found 0.001068
NBN c.G340T p.V114F Not found Not found
RET c.C2249G p.A750G Not found 0.000008238
XRCC3 c.C260T p.P87L Not found 0.00006286
25/B50 POLH c.A2074G p.T692A DM Xeroderma pigmentosum 0.0001824
Tp53 c.673-36G > C DFP Breast cancer Not found
CTNNB1 c.A2315G p.N772S Not found 0.00003355
POLD1 c.C519G p.S173R Not found 0.009212
26/D1 ARL11 c.G446A p.W149X DP Association with cancer 0.009898
MSH2 c.T1182G p.F394L Not found 0.00001648
27/D4 CHEK2 c.T470C p.I157T DFP Li-Fraumeni syndrome Not found
28/D5 CDH1 c.G2387A p.R796Q Not found 0.00003300
29/D6 BUB1B c.A1535G p.E512G Not found 0.000008239
30/D7 APC c.C2876T p.S959F Not found Not found
BRCA1 c.G131T p.C44F DM Breast and/or ovarian cancer Not found
PRF1 c.G3A p.M1I DM Haemophagocytic lymphohistiocytosis, familial Not found
31/D8 TP53 c.G469A p.V157I DM Sarcoma, adult-onset 0.00005776
32/III_4 CDH1 c.G3A p.M1I DM Gastric cancer Not found
BRCA2 c.C4061T p.T1354M DM Breast cancer 0.000008328
BRCA2 c.G4258T p.D1420Y DM? Breast and/or ovarian cancer 0.006796
33/D12 CDH1 c.A160G p.R54G Not found 0.00005916
34/D13 BRCA2 c.G223C p.A75P DM? Breast cancer 0.0001650
  1. DM disease-causing mutation, DM? likely disease-causing mutation, DP disease-associated polymorphism, FP in vitro or in vivo functional polymorphism, DFP disease-associated polymorphism with additional functional evidence