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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