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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.