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Table 3 Thirty-six mutations in the twelve genes that can be found in 98 CRC cases

From: Exome sequencing in one family with gastric- and rectal cancer

Chrom:Positiona

Ref

Obs

dbSNP

Func

Gene

Exonic function

1000G

249 patients

98 CRC casesb

F1

F2

F3

F4

F5

c

d

e

3:137786496

G

A

 

exonic

DZIP1L

stopgain SNV

  

0.0051

N

-

-

N

D

  

1

3:137790616

C

T

rs150466957

exonic

DZIP1L

ns SNV

0.0009

 

0.0051

N

D

P

N

N

  

1

3:137813726

G

A

rs148594666

exonic

DZIP1L

ns SNV

0.0009

 

0.0051

C

T

P

N

N

1

  

3:142539852

C

T

 

exonic

PCOLCE2

ns SNV

 

0.002

0.0051

C

T

B

D

N

  

1

3:142548681

C

T

rs140721173

exonic

PCOLCE2

ns SNV

0.0009

0.002

0.0051

N

T

B

D

D

  

1

3:151163838

T

C

rs34114908

exonic

IGSF10

ns SNV

0.01

0.01

0.0357

N

D

B

N

N

 

2

3

3:151165241

G

C

rs142202060

exonic

IGSF10

ns SNV

0.0005

0.004

0.0102

C

D

P

N

N

 

1

 

3:151165532

G

C

rs35667704

exonic

IGSF10

ns SNV

0.0037

0.0141

0.0153

N

D

P

N

N

 

1

1

3:151166124

A

G

rs146828199

exonic

IGSF10

ns SNV

  

0.0051

C

D

D

N

D

  

1

9:107332377

T

A

rs76017116

exonic

OR13C8

ns SNV

0.01

0.004

0.0153

C

D

B

D

D

  

3

9:111954616

C

T

rs199718023

exonic

EPB41L4B

ns SNV

  

0.0051

C

D

B

N

N

  

1

9:111954622

C

T

rs201059767

exonic

EPB41L4B

ns SNV

  

0

C

D

B

N

N

  

1

9:112029768

C

T

 

exonic

EPB41L4B

ns SNV

  

0.0051

C

T

B

N

-

1

  

9:112082510

C

T

rs117569740

exonic

EPB41L4B

ns SNV

0.14

0.1124

0.1531

C

D

B

-

-

8

4

14

9:139345847

G

A

rs45519739

exonic

SEC16A

ns SNV

0.01

 

0.0153

     

1

 

1

9:139348749

G

A

rs79974534

exonic

SEC16A

ns SNV

0.01

0.0141

0.0306

     

1

1

2

9:139360781

G

A

rs199798606

exonic

SEC16A

ns SNV

 

0.004

0.0051

       

1

9:139368953

G

A

rs3812594

exonic

SEC16A

ns SNV

0.16

0.2048

0.2653

     

9

9

17

9:139369066

G

A

rs148167113

exonic

SEC16A

ns SNV

0.01

0.004

0.0153

     

1

 

2

9:139369091

C

T

rs11788702

exonic

SEC16A

ns SNV

0.0005

 

0.0051

       

1

9:139369408

C

T

rs200238338

exonic

SEC16A

ns SNV

  

0.0051

     

1

  

9:139369816

G

C

rs200394508

exonic

SEC16A

ns SNV

  

0.0204

     

1

 

3

9:139370955

del9

-

 

exonic

SEC16A

non-frameshift deletion

 

0.008

0.0153

     

1

 

2

9:139401233

C

T

rs61751543

exonic

NOTCH1

ns SNV

0.01

0.01

0.0204

C

T

D

D

D

2

 

2

9:139409775

C

T

rs201077220

exonic

NOTCH1

ns SNV

0.0009

 

0.0051

C

T

B

-

D

  

1

12:10954258

C

T

rs619381

exonic

TAS2R7

ns SNV

0.07

0.0884

0.1173

N

T

D

N

N

1

5

12

12:10954583

A

T

rs139604652

exonic

TAS2R7

ns SNV

0.0032

 

0.0051

C

D

D

N

N

  

1

22:30742345

T

G

 

exonic

SF3A1

ns SNV

  

0.0102

C

T

P

D

D

  

2

22:30953280

C

T

rs55674628

exonic

GAL3ST1

ns SNV

0.01

0.0161

0.0204

C

T

B

N

N

2

 

3

22:38120338

G

A

 

exonic

TRIOBP

ns SNV

  

0.0051

N

-

D

-

-

1

  

22:38120542

C

T

rs142024473

exonic

TRIOBP

ns SNV

0.03

0.0201

0.0459

C

-

P

-

-

1

1

6

22:38120985

A

G

 

exonic

TRIOBP

ns SNV

  

0.0051

N

-

D

-

-

1

  

22:38121040

C

T

rs41296243

exonic

TRIOBP

ns SNV

0.01

0.0201

0.0306

N

-

P

-

-

2

1

2

22:38121795

C

T

rs200359708

exonic

TRIOBP

ns SNV

0.0018

 

0.0051

C

-

D

-

-

1

  

22:38122414

AG

-

 

exonic

TRIOBP

frameshift deletion

  

0.0051

       

2

22:38129388

G

A

rs34066624

exonic

TRIOBP

ns SNV

0.0023

0.008

0.0204

C

-

-

-

-

1

 

3

  1. aGRCh37 (hg19) coordinates
  2. b1000 Genomes version April 2012 (hg19)
  3. cNumber of families where only one individual was sequenced and had a mutation
  4. dNumber of families where at least two individuals were sequenced and the mutation segregated
  5. eNumber of families where at least two individuals were sequenced and the mutation did not segregate
  6. F1, Phylop; C, Conserved; N, Not conserved
  7. F2, SIFT; T, Tolerated; D, Deleterious
  8. F3, Polyphen2; D, Probably damaging; P, Possibly damaging; B, Benign
  9. F4, LRT; N, Neutral; D, Deleterious
  10. F5, MutationTaster; N, Polymorphism; D, Disease causing