Table 3. Mitochondrial DNA sequence changes in Leber hereditary optic neuropathy patients.
| Sample number | Nucleotide substitution | Codon Change | Amino acid change | Locus | Base substitution type | Type of mutation | Polyphen/SIFT score | Pathogenic | GenBank accession number if novel |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
*3460 G>A |
GCC>ACC |
p.A52T |
ND1 |
Transition |
NS |
1.646/0.00 |
YES |
NA |
| 2 |
4852 T>A |
CTG>CAG |
p.L128Q |
ND2 |
Transversion |
NS |
1.951/0.00 |
YES |
GU197845 |
| 3 |
4944 A>G |
ATC>GTC |
p.I159V |
ND2 |
Transition |
NS |
0.468/0.29 |
NO |
NA |
| 4 |
5004 T>C |
TTA>CTA |
p.L179L |
ND2 |
Transition |
SYN |
NA |
NA |
NA |
| 5 |
6032 G>A |
CAG>CAA |
p.Q43Q |
CO1 |
Transition |
SYN |
NA |
NA |
NA |
| 6 |
6320 T>C |
CCT>CCC |
p.P139P |
CO1 |
Transition |
SYN |
NA |
NA |
NA |
| 7 |
6734 G>A |
ATG>ATA |
p.M277M |
CO1 |
Transition |
SYN |
NA |
NA |
NA |
| 8 |
6908 T>C |
TCT>TCC |
p.S335S |
CO1 |
Transition |
SYN |
NA |
NA |
NA |
| 9 |
7702 G>A |
CTG>CTA |
p.L39L |
CO2 |
Transition |
SYN |
NA |
NA |
NA |
| 10 |
8155 G>A |
GGG>GGA |
p.G190G |
CO2 |
Transition |
SYN |
NA |
NA |
NA |
| 11 |
8668 T>C |
TGA>CGA |
p.W48R |
ATP6 |
Transition |
NS |
2.734/0.03 |
YES |
NA |
| 12 |
8684 C>T |
ACC>ATC |
p.T53I |
ATP6 |
Transition |
NS |
0.219/1.00 |
NO |
NA |
| 13 |
9254 A>G |
TGA>TGG |
p.W16W |
CO3 |
Transition |
SYN |
NA |
NA |
NA |
| 14 |
9767 C>T |
ACC>ACT |
p.T187T |
CO3 |
Transition |
SYN |
NA |
NA |
NA |
| 15 |
9966 G>A |
GTC>ATC |
p.V254I |
CO3 |
Transition |
NS |
0.293/0.46 |
NO |
NA |
| 16 |
10238 T>C |
ATT>ATC |
p.I60I |
ND3 |
Transition |
SYN |
NA |
NA |
NA |
| 17 |
10256 T>C |
GAT>GAC |
p.D66D |
ND3 |
Transition |
SYN |
NA |
NA |
NA |
| 18 |
10400 C>T |
ACC>ACT |
p.T114T |
ND3 |
Transition |
SYN |
NA |
NA |
NA |
| 19 |
10589 G>A |
CTG>CTA |
p.L40L |
ND4L |
Transition |
SYN |
NA |
NA |
NA |
| 20 |
*11778 G>A |
CGC>CAC |
p.R340H |
ND4 |
Transition |
NS |
2.608/0.00 |
YES |
NA |
| 21 |
12348 C>T |
CAC>CAT |
p.H4H |
ND5 |
Transition |
SYN |
NA |
NA |
GU197843 |
| 22 |
12477 T>C |
AGT>AGC |
p.S47S |
ND5 |
Transition |
SYN |
NA |
NA |
NA |
| 23 |
12681 T>C |
AAT>AAC |
p.N115N |
ND5 |
Transition |
SYN |
NA |
NA |
NA |
| 24 |
12732 T>C |
GTT>GTC |
p.V132V |
ND5 |
Transition |
SYN |
NA |
NA |
NA |
| 25 |
13151 T>C |
CTA>CCA |
p.L272P |
ND5 |
Transition |
NS |
0.175/0.21 |
No |
GU197844 |
| 26 |
14783 T>C |
TTA>CTA |
p.L13L |
CYB |
Transition |
SYN |
NA |
NA |
NA |
| 27 |
14950 C>T |
CAC>CAT |
p.H68H |
CYB |
Transition |
SYN |
NA |
NA |
GU197846 |
| 28 |
15067 T>C |
TTT>TTC |
p.F107F |
CYB |
Transition |
SYN |
NA |
NA |
NA |
| 29 |
15110 G>A |
GCA>ACA |
p.A122T |
CYB |
Transition |
NS |
0.401/0.65 |
NO |
NA |
| 30 | 15493 C>T | CTC>CTT | p.L249L | CYB | Transition | SYN | NA | NA | GU197847 |
Abbrevations: *Primary Leber hereditary optic neuropathy (LHON) mutations, SYN represents synonymous, NS represents Not synonymous, NA represents Not applicable Transition represents It is a mutation in which a purine/pyrimidine base pair is replaced with a base pair in the same purine/pyrimidine relationship (A:T>G:C or C:G>T:A). Transversion represents It is a mutation in which a purine/pyrimidine replaces a pyrimidine/purine base pair or vice versa (G:C>T:A or C:G, or A:T>T:A or C:G).