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