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Table 1 Variants with potential clinical significance. Putative somatic variants are identified as those with < 1% allele frequency in the 1000 genomes population and alternate allele frequency > 70% or < 30%, or those annotated in COSMIC

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

  1. aVariant annotated in the Catalogue of Somatic Mutations in Cancer (COSMIC)
  2. bVariant annotated ClinVar (NCBI Clinical Variant Database)
  3. cVariant frequencies of 0.5 ± 0.05 or 1.0 ± 0.05 may be germline
  4. dPolyphen algorithm score for predicting damaging mutations (non-Mendelian) (1 = most severe; http://genetics.bwh.harvard.edu/pph2/)
  5. eFrequency reported in the combined 1000 genomes database