In addition to the identical T3866C mutation, as shown in Supplemental Table 2 (see Supplementary Material and
Supplementary Table 2), these probands exhibited distinct sets of mtDNA polymorphism belonging to the Eastern Asian haplogroups D4a, M10a, and R, respectively.
24 Among 44, 44, and 39 variants of WZ510, WZ511, and WZ512 pedigrees, respectively, their mtDNA shared 22 identical variants. These variants were 13 known variants in the D-loop, 3 known variants in the 12S rRNA gene, 4 known variants in the 16S rRNA gene, 28 (2 novel and 26 known) silent variants, and 19 (2 novel and 17 known) missense mutations in the protein encoding genes.
34 These missense mutations are the C5178A (L237M) and A5466G (T333A) in the
ND2 gene; the G6915A (V338M) in the
CO1 gene; the C8414T (L17F) in the
A8 gene; the A8701G (T59A), T8821C (S99A), and A8860G (T112A) in the
A6 gene; the G9966A (V254I) in the
CO3 gene; the G10197A (A47T) and A10398G (T114A) in the
ND3 gene; the G13135A (A267T) and C13561A (L409M) in the
ND5 gene; the T14502C (I58V) in the
ND6 gene; and the C14766T (T7I), T14979C (I78T), T15071C (Y109H), A15218G (T158A), and A15326G (T194A) in the
Cytb gene. These variants in RNAs and polypeptides were further evaluated by phylogenetic analysis of these variants and sequences from 17 vertebrates including mouse,
36 bovine,
37 and
Xenopus laevis .
38 The CI of ND1 I187S mutation was 76.5%, which was above the threshold level to be of functional significance in terms of mitochondrial physiology.
39 Of other variants, CIs of ATP6 S99A and CO3 V254I variants of WZ511 pedigree, ND3 A47T variant of WZ510 pedigree, ND5 L409M and ND6 I58V variants of WZ512 family, and Cytb T158A variant of WZ511 and WZ512 pedigrees ranged from 76.4% to 100%. Allelic frequency showed that the ATP6 S99A and ND5 L409M variants were absent but CO3 V254I, ND3 A47T, ND6 I58V, and Cytb T158A variants were present among 2704 human mitochondrial genomes using the mtDB.
35 Furthermore, other variants were <70% CI, which was below the threshold level to be functional significantly in terms of mitochondrial physiology, proposed by Wallace (2005).
39 These data suggest that the ATP6 S99A and ND5 L409M variants but not other variants may be functional significantly.