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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.