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. 2014 Jan 2;2:1. doi: 10.1186/2051-5960-2-1

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.

HHS Vulnerability Disclosure