Table 1. The nonsynonymous and tRNA private variants in complete mtDNA sequences with m.3635G>A.
| Samplea | Private variant (amino acid change) | Gene | Reported (population context)b | Reported (disease context)b | Haplogroup-specific variantc | Variant frequencyd | Conservation Index (CI)e | Pathogenic scoref |
|---|---|---|---|---|---|---|---|---|
| Allg |
m.3635G>A (p.S110N) |
MT-ND1 |
No |
Yes |
No |
4/15859 |
1 |
0.797 |
| Le329, Le337 |
m.5301A>G (p.I278V) |
MT-ND2 |
Yes |
Yes |
Yes (M6, D5, H1e1a1) |
125/15859 |
0.75 |
0.311 |
| |
m.14063T>C (p.I576T) |
MT-ND5 |
Yes |
Yes |
No |
12/15859 |
0.25 |
0.582 |
| |
m.12811T>C (p.Y159H) |
MT-ND5 |
Yes |
Yes |
Yes (H3h, A2h1, M7b1’2’4–8) |
124/15859 |
0.58 |
0.587 |
| |
m.15237T>C (p.I164T) |
MT-CYB |
Yes |
No |
No |
2/15859 |
1 |
0.508 |
| Le569 |
m.5773G>A |
MT-TC |
Yes |
Yes |
Yes (L0d3, A5a1a1, M13a, M24, M39a, L3b, D4i1, J1c1b1, H4a1b, K1a2a, C1c1b, H4a1a3) |
220/15859 |
0.25 |
|
|
EU807741.1 |
m.8551T>C (p.F9L) |
MT-ATP6 |
Yes |
Yes |
No |
10/15859 |
1 |
0.745 |
|
FJ969382.1 |
m.7868C>T (p.L95F) |
MT-CO2 |
Yes |
Yes |
No |
12/15859 |
0.15 |
0.539 |
| |
m.9071C>T (p.S182L) |
MT-ATP6 |
Yes |
Yes |
Yes (H16c) |
5/15859 |
0.65 |
0.223 |
| |
m.12358A>G (p.T8A) |
MT-ND5 |
Yes |
Yes |
Yes (B4e, P4a, N1a1b, M7d, N9a, U5a1b1d, M12a, M27, D4b2b2, D4j1a) |
216/15859 |
0.77 |
0.265 |
| FJ969383.1 | m.3421G>A (p.V39I) | MT-ND1 | Yes | Yes | Yes (D4n, HV1a3, W3a1a1, H81a) | 32/15859 | 0.37 | 0.413 |
aThe complete mtDNA genomes of Le131, Le834 and Le1143 contained no private non-synonymous and mt-tRNA variants and was not included in the table. bThe uniqueness of each variant was searched according to the described strategy [26] on 10 August, 2012 (e.g., both “G3635A mtDNA” and “3635G>A mtDNA” were queried). cThe haplogroup-specific variant was determined according to the available global mtDNA phylogenetic tree at the Phylotree (mtDNA tree Build 14, 5 Apr 2012). The haplogroup status as it defined in that tree was indicated in round brackets. d The variant frequency was calculated as the number of occurrences of each variant in 15,859 complete or near complete mtDNA sequences that were summarized by MitoTool project [24]. eThe conservation index which was defined by Ruiz-Pesini et al. [30], was calculated by using MitoTool [24] concerning 43 primate species. A CI value of 0.419 meant 41.9% of 43 primate species share the same allele with the revised Cambridge Reference Sequence (rCRS) [18] (GenBank accession number NC_012920). fThe pathogenicity score was referred to the recent study of Pereira et al. [27]. The score ranges from 0 to 1. Higher pathogenicity score is associated with greater possibility that the variant is pathogenic. gAll samples contain m.3635G>A.