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Table 2 MtDNA variants identified within the coding region of 12 GBM cell lines

From: The identification of mitochondrial DNA variants in glioblastoma multiforme

  

Percentage change in variant (%)

   

MutPred

Reference position

Variant change

HSR-GBM1

GBM L1

GBM L2

GBM 4

GBM 6

CSC 014

CSC 020

NO7 152

SF-767

U87MG

HK301

BAH1

Gene region

Amino acid change

SNPs & GO

Probability of deleterious mutation

Top 5 predicted features caused by the amino acid mutation

6422

C→T

3.8

           

COX I

Syn (P)

-

-

 

6999

G→A

6.5

           

V366M

Neutral, RI 4, uniprot P00395

0.454

Loss of stability (P = 0.0688)

Loss of sheet (P = 0.0817)

Loss of catalytic residue at V366 (P = 0.1011)

Loss of glycosylation at S362 (P = 0.2022)

Gain of loop (P = 0.4661)

8251

G→A

 

43.5

 

50.8

        

COX II

Syn (G)

-

-

 

8252

C→A

 

55.5

 

46.8

        

P223T

Neutral, RI 9, uniprot P00403

0.327

Gain of glycosylation at P223 (P = 0.1135)

Loss of disorder (P = 0.1694)

Loss of catalytic residue at G222 (P = 0.2169)

Loss of phosphorylation at T226 (P = 0.3735)

Loss of helix (P = 0.3949)

10473

C→G

     

4.3

      

ND4L

P2A

Neutral, RI 9, uniprot P03901

0.344

Loss of disorder (P = 0.0496)

Loss of catalytic residue at L3 (P = 0.1395)

Gain of helix (P = 0.2684)

Loss of loop (P = 0.3664)

Loss of phosphorylation at Y5 (P = 0.4053)

10814

A→C

 

6.0

 

5.3

  

5.0

5.2

    

ND4

K19Q

Neutral, RI 8, uniprot P03905

0.551

Loss of methylation at K19 (P = 0.0012)

Loss of ubiquitination at K19 (P = 0.0283)

Loss of MoRF binding (P = 0.134)

Gain of helix (P = 0.2684)

Loss of catalytic residue at K19 (P = 0.2966)

11361

T→C

     

6.0

      

M201T

Neutral, RI 5, uniprot P03905

0.706

Loss of stability (P = 0.0853)

Gain of ubiquitination at K206 (P = 0.1204)

Gain of catalytic residue at M201 (P = 0.1253)

Gain of methylation at K206 (P = 0.1903)

Loss of MoRF binding (P = 0.2081)

11512

C→A

 

6.0

 

9.6

 

11.0

6.4

15.2

    

N251K

Neutral, RI 4, uniprot P03905

0.495

Gain of methylation at N251 (P = 0.0194)

Gain of MoRF binding (P = 0.0632)

Loss of stability (P = 0.0709)

Loss of ubiquitination at K255 (P = 0.0768)

Gain of solvent accessibility (P = 0.0837)

11674

C→T

   

3.5

        

Syn (T)

-

-

 

12101

T→C

   

3.8

 

3.1

 

4.2

    

S448P

Neutral, RI 7, uniprot P03905

0.484

Loss of helix (P = 0.0093)

Gain of loop (P = 0.0321)

Gain of relative solvent accessibility (P = 0.09)

Gain of sheet (P = 0.1451)

Gain of catalytic residue at L447 (P = 0.1502)

12102

C→T

   

3.7

   

3.2

    

S448F

Neutral, RI 3, uniprot P03905

0.472

Loss of disorder (P = 0.0619)

Gain of helix (P = 0.2059)

Loss of loop (P = 0.2897)

Loss of phosphorylation at S448 (P = 0.5302)

Gain of catalytic residue at S448 (P = 0.5425)

12877

G→C

        

27.7

   

ND5

G181R

Disease, RI 7, Uniprot P03915

0.795

Loss of catalytic residue at I183 (P = 0.1945)

Gain of MoRF binding (P = 0.2553)

Gain of methylation at G181 (P = 0.3559)

Loss of helix (P = 0.4763)

Loss of stability (P = 0.5598)

13043

C→T

         

3.3

  

A236V

Neutral, RI 3, Uniprot P03915

0.786

Loss of glycosylation at P234 (P = 0.0757)

Loss of disorder (P = 0.0789)

Gain of helix (P = 0.132)

Loss of phosphorylation at T241 (P = 0.2504)

Loss of loop (P = 0.2897)

13061

C→A

      

4.0

     

P242Q

Disease, RI 0, uniprot P03915

0.776

Loss of glycosylation at P242 (P = 0.035)

Loss of phosphorylation at T241 (P = 0.1079)

Loss of disorder (P = 0.1807)

Loss of catalytic residue at E238 (P = 0.1978)

Loss of helix (P = 0.2271)

14159

C→G

  

4.1

         

ND6

R172P

Disease, RI 3, uniprot P03923

0.423

Loss of methylation at R172 (P = 0.0305)

Gain of catalytic residue at R172 (P = 0.0632)

Loss of sheet (P = 0.0817)

Loss of stability (P = 0.126)

Gain of disorder (P = 0.1619)

14160

G→C

  

4.0

3.5

3.3

7.5

 

4.3

3.2

 

8.1

5.0

R172G

Neutral, RI 2, uniprot P03923

0.442

Loss of methylation at R172 (P = 0.0305)

Loss of stability (P = 0.0532)

Loss of sheet (P = 0.0817)

Gain of disorder (P = 0.1578)

Gain of loop (P = 0.2045)

14426

C→T

     

8.9

      

G85E

Neutral, RI 7, uniprot P03923

0.364

Loss of glycosylation at S84 (P = 0.0357)

Gain of solvent accessibility (P = 0.0456)

Loss of catalytic residue at V86 (P = 0.1017)

Gain of disorder (P = 0.1294)

Gain of loop (P = 0.2045)

15264

C→T

14.1

           

CYTB

P173L

Disease, RI 4, uniprot P00156

0.361

Loss of relative solvent accessibility (P = 0.0793)

Loss of solvent accessibility (P = 0.089)

Gain of methylation at R177 (P = 0.1226)

Loss of glycosylation at S172 (P = 0.1763)

Loss of disorder (P = 0.2084)

15267

C→G

20.5

           

T174S

Disease, RI 3, uniprot P00156

0.866

Gain of glycosylation at T174 (P = 0.0587)

Gain of disorder (P = 0.0665)

Loss of catalytic residue at T174 (P = 0.1513)

Loss of methylation at R177 (P = 0.2045)

                  

Loss of sheet (P = 0.3635)

  1. In silico analysis was performed using the online tools SNPs & GO and MutPred to predict the impact these variants exert on the corresponding protein of interest. Variants that have not been previously reported are in bold.