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Table 4 Summary of mutations

From: Comprehensive genomic evaluation of advanced and recurrent breast cancer patients for tailored precision treatments

  

Functional effect

   

Gene

Total number

Nonsense

Missense

Frameshift

Non-frameshift

Splice

Allele fraction*

Amplification

Loss

pLI

score

CADD

score*

PIK3CA

9

 

3

 

6

 

0.3096 (0.0101–0.5875)

  

1

3.332(0.797-39)

TP53

7

1

3

2

  

0.5337 (0.0325–0.8020)

  

0.53

23(0.108-34)

MYC

4

      

4

 

0.99

 

PTEN

3

1

 

1

  

0.8385, 0.5590

 

1

0.26

24.8, 2.877

CDH1

3

        

0.15

 

CDKN2A

2

       

2

0.32

 

CDKN2B

2

       

2

0.01

 

ZNF217

2

      

2

 

1

 

MDM4

2

      

2

 

1

 

IKBKE

2

 

1

   

0.0572

1

 

unknown

3.158

PIK3C2B

2

      

2

 

1

 

MTAP

2

       

2

0

 

FGFR1

2

      

2

 

1

 

ZNF703

2

      

2

 

0.36

 

NSD3

2

      

2

 

1

 

SF3B1

2

 

2

   

0.3314, 0.2628

  

1

5.916

TBX3

2

  

2

  

0.3940, 0.2493

  

0.98

5.758, 0.935

FGF3

2

      

2

 

0

 

FGF4

2

      

2

 

0.14

 

FGF19

2

      

2

 

0.57

 

SDHA

2

 

1

1

  

0.4379, 0.5006

  

0

0.704, 24.9

  1. *Median (range) was given when there were > 3 cases. pLI: probability of being loss-of-function intolerant; CADD: combined annotation-dependent depletion
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