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Table 3 Number of carriers with loss-of-function and missense variants detected in case and control cohorts

From: Evaluating the breast cancer predisposition role of rare variants in genes associated with low-penetrance breast cancer risk SNPs

Gene

Selection criteria

Number of carriers with loss-of-function variants

Number of carriers with missense variants

Case

Control

p Valuea

OR

95% CI

Case

Control

p Valuea

OR

95% CI

TET2

GWAS proposed

5

2

0.456

2.27

0.37–23.87

20

18

1

1.01

0.50–2.03

NRIP1

GWAS proposed

3

0

0.251

Und

0.37–∞

21

17

0.632

1.12

0.56–2.28

RAD51B

GWAS proposed

2

0

0.501

Und

0.17–∞

6

4

0.756

1.36

0.32–6.57

SNX32

Neighbouring genes

2

0

0.501

Und

0.17–∞

3

6

0.323

0.45

0.07–2.12

ZNF226

Neighbouring genes

2

2

1

0.91

0.07–12.5

24

18

0.640

1.21

0.63–2.39

ADAM29

GWAS proposed

1

0

1

Und

0.02–∞

13

11

1

1.07

0.44–2.65

CASP8

GWAS proposed

1

0

1

Und

0.02–∞

8

2

0.113

3.64

0.72–35.26

CDKN2A

GWAS proposed

1

0

1

Und

0.02–∞

3

3

1

0.91

0.12–6.77

DCLRE1B

Neighbouring genes

1

1

1

0.91

0.01–71.08

7

6

1

1.06

0.30–3.82

FTO

GWAS proposed

1

0

1

Und

0.02–∞

10

11

0.668

0.82

0.31–2.14

LGR6

GWAS proposed

1

0

1

Und

0.02–∞

16

8

0.217

1.82

0.73–4.94

MUS81

Neighbouring genes

1

1

1

0.91

0.01–71.08

8

9

0.808

0.80

0.27–2.36

NFRKB

Neighbouring genes

1

1

1

0.91

0.01–71.08

17

12

0.577

1.29

0.58–2.97

PDE4D

GWAS proposed

1

0

1

Und

0.02–∞

6

3

0.512

1.81

0.39–11.24

SETMAR

Neighbouring genes

1

2

0.607

0.45

0.01–8.70

7

3

0.349

2.12

0.48–12.73

SLC4A7

GWAS proposed

1

0

1

Und

0.02–∞

14

10

0.682

1.27

0.52–3.21

USHBP1

Neighbouring genes

1

1

1

0.91

0.01–71.08

14

11

0.841

1.15

0.48–2.82

CDKN2B

GWAS proposed

0

1

0.475

0

0–35.30

1

1

1

0.91

0.01–71.08

TCF7L2

GWAS proposed

0

1

0.475

0

0–35.30

5

8

0.406

0.56

0.14–1.96

TPK1

Neighbouring genes

0

1

0.475

0

0–35.30

2

2

1

0.91

0.07–12.50

ZNF283

Neighbouring genes

–

–

–

–

–

17

6

0.057

2.59

0.97–8.06

HNF4G

GWAS proposed

–

–

–

–

–

4

1

0.377

3.63

0.36–178.82

TERT

GWAS proposed

–

–

–

–

–

5

6

0.765

0.75

0.18–2.97

UNC13A

Neighbouring genes

–

–

–

–

–

17

8

0.158

1.94

0.79–5.21

LSP1

GWAS proposed

–

–

–

–

–

11

15

0.327

0.66

0.27–1.55

XRCC1

Neighbouring genes

–

–

–

–

–

6

12

0.153

0.45

0.14–1.30

ZMIZ1

GWAS proposed

–

–

–

–

–

15

11

0.694

1.24

0.53–3.00

EMID1

Neighbouring genes

–

–

–

–

–

11

8

0.654

1.25

0.46–3.59

FGFR2

GWAS proposed

–

–

–

–

–

4

4

1

0.91

0.17–4.87

CCDC88C

GWAS proposed

–

–

–

–

–

38

45

0.219

0.76

0.47–1.20

ITPR1

Neighbouring genes

–

–

–

–

–

17

20

0.507

0.77

0.37–1.55

MKL1

GWAS proposed

–

–

–

–

–

26

19

0.547

1.24

0.66–2.40

CHST9

GWAS proposed

–

–

–

–

–

7

9

0.617

0.70

0.22–2.13

PEX14

GWAS proposed

–

–

–

–

–

9

6

0.613

1.36

0.43–4.66

PAX9

GWAS proposed

–

–

–

–

–

3

7

0.207

0.39

0.06–1.70

PTHLH

GWAS proposed

–

–

–

–

–

3

1

0.626

2.72

0.22–142.85

CDCA7

GWAS proposed

–

–

–

–

–

5

3

0.729

1.51

0.29–9.76

MAP3K1

GWAS proposed

–

–

–

–

–

20

11

0.206

1.66

0.75–3.85

RANBP9

GWAS proposed

–

–

–

–

–

10

5

0.309

1.82

0.56–6.80

DNAJC1

GWAS proposed

–

–

–

–

–

8

9

0.808

0.80

0.27–2.36

TOX3

GWAS proposed

–

–

–

–

–

7

7

1

0.90

0.27–3.03

EPB41L5

Neighbouring genes

–

–

–

–

–

8

8

1

0.90

0.29–2.78

ESR1

GWAS proposed

–

–

–

–

–

3

6

0.323

0.45

0.07–2.12

MDM4

GWAS proposed

–

–

–

–

–

7

3

0.349

2.12

0.48–12.73

CDYL2

GWAS proposed

–

–

–

–

–

11

5

0.217

2

0.64–7.37

TNP1

Neighbouring genes

–

–

–

–

–

0

2

0.226

0

0–4.82

BABAM1

Neighbouring genes

–

–

–

–

–

4

3

1

1.21

0.20–8.27

TGFBR2

GWAS proposed

–

–

–

–

–

4

3

1

1.21

0.20–8.27

ELL

GWAS proposed

–

–

–

–

–

9

5

0.430

1.63

0.49–6.23

NF2

Neighbouring genes

–

–

–

–

–

12

5

0.150

2.19

0.71–7.95

KCNN4

Neighbouring genes

–

–

–

–

–

8

4

0.393

1.82

0.49–8.27

DLX2

Neighbouring genes

–

–

–

–

–

7

4

0.553

1.59

0.40–7.42

KAT5

Neighbouring genes

–

–

–

–

–

3

2

1

1.36

0.16–16.29

COX11

GWAS proposed

–

–

–

–

–

2

1

1

1.81

0.09–106.93

EBF1

GWAS proposed

–

–

–

–

–

2

3

0.673

0.60

0.05–5.27

RAD23B

Neighbouring genes

–

–

–

–

–

0

1

0.475

0

0–35.30

GWAS proposed genes

–

17

4

0.008

3.89

1.26–15.95

287

251

0.679b

1.05

0.86–1.28

Neighbouring genes

–

9

9

1

0.90

0.32–2.58

168

138

0.392b

1.12

0.87–1.44

Total

–

26

13

0.077

1.83

0.90–3.90

406

353

0.512b

1.07

0.89–1.28

  1. Abbreviations: GWAS Genome-wide association study, Und undefined
  2. aFisher’s exact test, two-sided
  3. bPearson’s chi-square test with the Yates correction