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) |