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Table 2 Frequencies of NMDpositive variants in hereditary cancer, primary ciliary dyskinesia (PCD), and arrhythmia/cardiomyopathy genes in ExAC

From: Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation

  

Variant allele frequencies in ExAC:

Gene

Inheritance

<0.005%

0.005–0.01%

0.01–0.05%

0.05–0.1%

≥0.1%

Hereditary cancer

  APC

Dominant

6

-

-

-

-

  ATM

Recessive

104

1

-

-

-

  BARD1

Dominant

22

-

-

-

-

  BLM

Recessive

38

2

1

-

-

  BMPR1A

Dominant

3

1

-

-

-

  BRCA1

Dominant

67

-

2

-

-

  BRCA2

Dominant

103

2

1

-

-

  BRIP1

Recessive

32

-

1

-

-

  CDH1

Dominant

5

-

-

-

-

  CDKN2A

Dominant

4

-

-

-

-

  CHEK2

Dominant

29

3

2

-

1

  CTRC

Dominant

11

1

-

-

-

  EPCAM

Recessive

9

1

-

-

-

  FANCC

Recessive

23

1

-

-

-

  MEN1

Dominant

-

-

-

-

-

  MLH1

Dominant

5

-

-

-

-

  MRE11A

Recessive

18

1

-

-

-

  MSH2

Dominant

7

1

-

-

-

  MSH6

Dominant

25

-

1

-

-

  MUTY

Recessive

19

3

2

-

1

  NBN

Recessive

33

1

1

-

-

  NF1

Dominant

23

1

-

-

-

  PALB2

Dominant

35

2

1

-

-

  PMS2

Dominant

32

-

-

-

-

  PTCH1

Dominant

2

-

-

-

-

  PTEN

Dominant

2

-

-

-

-

  RAD50

Recessive

42

2

3

-

-

  RAD51C

Recessive

19

3

-

-

-

  SMAD4

Dominant

2

-

-

-

-

  SPINK1

Dominant

1

-

1

-

-

  STK11

Dominant

-

-

-

-

-

  TP53

Dominant

1

-

-

-

-

  VHL

Dominant

-

-

-

-

-

Primary ciliary dyskinesia

  ARMC4

Recessive

36

3

-

-

-

  C21orf59

Recessive

7

1

1

-

-

  CCDC103

Recessive

3

-

-

-

-

  CCDC114

Recessive

6

-

-

-

-

  CCDC151

Recessive

16

1

-

-

-

  CCDC39

Recessive

22

2

-

-

-

  CCDC40

Recessive

32

1

1

-

-

  CCDC65

Recessive

17

-

1

-

-

  CCNO

Recessive

-

-

-

-

-

  DNAAF1

Recessive

19

2

1

-

-

  DNAAF2

Recessive

12

-

-

-

-

  DNAAF3

Recessive

16

2

1

-

-

  DNAH11

Recessive

80

1

2

-

-

  DNAH5

Recessive

113

-

2

-

-

  DNAI1

Recessive

15

-

1

-

-

  DNAI2

Recessive

21

1

1

-

-

  DNAL1

Recessive

3

-

-

-

-

  DRC1

Recessive

22

-

2

-

-

  DYX1C1

Recessive

18

1

-

-

-

  RPGR

Recessive

1

-

-

-

-

  RSPH1

Recessive

9

1

2

-

-

  RSPH4A

Recessive

27

1

-

-

-

  RSPH9

Recessive

4

-

-

-

-

  SPAG1

Recessive

21

2

-

-

-

  ZMYND10

Recessive

16

-

-

-

-

Arrhythmia and cardiomyopathy

  BAG3

Dominant

2

-

-

-

-

  CACNA1C

Dominant

6

-

-

-

-

  CASQ2

Recessive

15

-

-

-

-

  DES

Recessive

5

-

-

-

-

  DSC2

Dominant

13

-

-

-

-

  DSG2

Dominant

19

-

-

-

-

  DSP

Recessive

21

-

-

-

-

  FHL1

Dominant

-

-

-

-

-

  HCN4

Dominant

5

-

-

-

-

  JUP

Recessive

7

-

-

-

-

  KCNE1

Dominant

-

-

-

-

-

  KCNH2

Dominant

5

-

2

-

-

  KCNQ1

Dominant

15

-

1

-

-

  LAMP2

Dominant

-

-

-

-

-

  LMNA

Dominant

1

-

-

-

-

  MYBPC3

Dominant

17

-

-

-

-

  NKX2-5

Dominant

1

-

-

-

-

  PKP2

Dominant

18

-

1

-

-

  PLN

Dominant

-

-

-

-

-

  SCN5A

Dominant

9

-

-

-

-

  TRDN

Recessive

6

1

2

-

-

  1. All NMDpositive variants for genes associated with hereditary cancer, primary ciliary dyskinesia, and arrhythmia/cardiomyopathy were binned based on their allele frequencies in the ExAC dataset. In all genes listed, loss of protein function has been established as the mechanism of disease. Several of the genes listed are associated with both dominant and recessive inheritance patterns; the listed inheritance patterns are specifically for those associated with the disorders most relevant to the clinical area, and the mechanism of disease is loss of function. For example, BRCA2 is associated with autosomal dominant hereditary breast and ovarian cancer, as well as autosomal recessive Fanconi anemia. DES and DSP genes are associated with both dominant and recessive arrhythmia and cardiomyopathy disorders. However, the loss-of-function mechanism has only been firmly established with the recessive disorders
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Genome Medicine

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