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Table 4 Variants identified in the coding region of the mitochondrial genome in normal brain tissue samples

From: The identification of mitochondrial DNA variants in glioblastoma multiforme

   

Percentage change in variant (%)

   

MutPred

Reference position

Reference

Variant

03-965

04-273

05-470

07-104

07-445

07-635

08-012

08-026

09-005

09-152

16-1

22-1

20-1

Gene region

Amino acid change

SNPs & GO

Probability of deleterious mutation

Top 5 predicted features caused by amino acid mutation

4646

T

C

        

3.4

    

ND2

Syn (Y)

-

  

4701

A

T

   

4.8

         

N78Y

Neutral, RI 7, Uniprot P03891

0.329

 

4703

T

C

   

4.8

         

Syn (N)

-

  

4878

G

A

        

4.6

    

A137T

Neutral, RI 5

0.786

 

4879

C

G

        

5.0

    

A137G

Neutral, RI 5

0.78

Loss of stability (P = 0.0465)

6146

A

G

        

3.1

    

COX I

Syn (W)

-

  

8497

A

G

 

12.5

      

4.8

    

ATP8

Syn (M)

-

  

8630

A

G

          

3.7

  

ATP6

K35 Stop

Uniprot P00846

  

8756

T

C

       

6.5

     

I77T

Neutral, RI 5

0.684

Loss of stability (P = 0.0062)

8790

G

A

    

18.4

        

Syn (L)

-

  

8994

G

A

       

4.7

     

Syn (L)

-

  

9070

T

G

        

6.2

    

S182A

Neutral RI 5

0.162

Loss of glycosylation at S182 (P = 0.0094)

9258

C

T

    

3.2

        

COX III

Syn (L)

-

  

9526

C

G

 

5.0

   

3.8

       

A107G

Neutral, RI 5, Uniprot P00414

0.667

Loss of stability (P = 0.0332)

9528

C

A

 

9.9

6.4

   

4.8

      

P108T

Neutral, RI 2

0.731

 

9558

C

A

    

5.8

  

3.6

     

P118T

Disease, RI 3

0.579

Loss of catalytic residue at P117 (P = 0.0195)

Gain of glycosylation at P118 (P = 0.0283)

10398

A

G

  

5.4

          

ND3

T114A

Neutral, RI 10, Uniprot P03897

0.071

 

10993

G

A

  

4.6

          

ND4

Syn (M)

-

  

11332

C

T

        

3.4

    

Syn (A)

-

  

11467

A

G

        

3.1

    

Syn (L)

-

  

11516

C

A

      

4.9

      

L253M

Neutral, RI 7, Uniprot P03905

0.369

 

11725

A

T

      

3.0

      

Syn (T)

-

  

11791

C

T

          

11.8

  

Syn (L)

   

12719

T

C

3.2

            

ND5

M128T

Disease, RI 2, Uniprot P03915

0.795

Loss of stability (P = 0.0126)

12774

C

T

          

9.3

  

Syn (G)

   

13984

C

T

         

3.7

   

Syn (L)

-

  

13985

T

C

  

3.1

     

3.1

3.7

   

L550P

Neutral, RI 1

0.457

Gain of loop (P = 0.0013)

Loss of helix (P = 0.0041)

Gain of catalytic residue at P549 (P = 0.0244)

Gain of glycosylation at L550 (P = 0.0364)

Gain of relative solvent accessibility (P = 0.0479)

14155

C

T

         

3.8

   

ND6

Syn (G)

-

  

14159

C

G

      

12.5

      

R172P

Disease, RI 3, Uniprot P03923

0.423

Loss of methylation at R172 (P = 0.0305)

14160

G

C

    

8.1

 

12.5

      

R172G

Neutral, RI 2

0.442

Loss of methylation at R172 (P = 0.0305)

14770

C

A

           

8.0

 

CYT B

N8K

Neutral RI 1, Uniprot P00156

0.446

Gain of methylation at N8 (P = 0.0039)

Gain of MoRF binding (P = 0.0159)

Gain of ubiquitination at N8 (P = 0.0452)

14823

A

C

    

4.0

        

N26T

Disease, RI 6

0.752

 

14857

T

C

      

3.8

      

Syn (L)

-

  

14861

G

T

      

3.6

      

A39S

Neutral, RI 5

0.33

 

14866

C

T

        

5.4

    

Syn (C )

-

  

15287

T

C

    

26.9

        

F181L

Neutral, RI 3

0.617

 

15452

C

A

  

3.2

          

L236I

Neutral, RI 7

0.307

 

15579

A

T

     

3.7

       

Y278F

Disease, RI 6

0.796

 

15693

T

C

        

4.9

     

M316T

Neutral, RI 8

0.312

 
  1. Variants represented those that were present at or above the 3% mutation threshold selection criteria. Variants that have not been previously reported are in bold. Predictions on the effects of amino acid substitutions were performed using MutPred and SNPs & GO online tools.