Mitochondrial DNA variant m.15218A > G in Finnish epilepsy patients who have maternal relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus

Abstract

Background: Mitochondrial diseases caused by mutations in mitochondrial DNA (mtDNA) affect tissues with high energy demand. Epilepsy is one of the manifestations of mitochondrial dysfunction when the brain is affected. We have studied here 79 Finnish patients with epilepsy and who have maternal first- or second-degree relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus.

Methods: The entire mtDNA was studied by using conformation sensitive gel electrophoresis and PCR fragments that differed in mobility were directly sequenced.

Results: We found a common nonsynonymous variant m.15218A > G (p.T158A, MTCYB) that occurs in haplogroup U5a1 to be more frequent in patients with epilepsy. The m.15218A > G variant was present in five patients with epilepsy and in four out of 403 population controls (p = 0.0077). This variant was present in two branches in the phylogenetic network constructed on the basis of mtDNA variation among the patients. Three algorithms predicted that m.15218A > G is damaging in effect.

Conclusions: We suggest that the m.15218A > G variant is mildly deleterious and that mtDNA involvement should be considered in patients with epilepsy and who have a maternal history of epilepsy, sensorineural hearing impairment or diabetes mellitus.

Figure 1

Phylogenetic network based on mtDNA coding region sequences in 79 patients with epilepsy and with a maternal history of epilepsy, SNHI or diabetes mellitus. Nodes represent patients. Inside the nodes, patients are identified by numbers 1-79. Outgroup is an African sequence [GenBank: AF346980]; CRS is the revised Cambridge Reference Sequence [GenBank: NC_012920]. Unless marked otherwise, mtDNA variants are transitions. Superscripts indicate transversions and novel mutations. @ = back mutation, * = heteroplasmic mutation, followed by patient number in parenthesis if required. D9bp = deletion spanning the positions m.8281 and m.8289. Nonsynonymous variants are in red font, underlined red variants were concordantly predicted to be pathogenic by PolyPhen-2, PMut and SIFT BLink analyses.

Figure 2

Phylogenetic network based on mtDNA D-loop sequences in 79 patients with epilepsy. Nodes represent patients. Inside the nodes, patients are identified by numbers 1-79. Outgroup is an African sequence [GenBank: AF346980]; CRS is the revised Cambridge Reference Sequence [GenBank: NC_012920]. Unless marked otherwise, mtDNA variants are transitions. Superscripts indicate transversions and novel mutations. @ = back mutation, * = heteroplasmic mutation.

Figure 3

Number of nonsynonymous variants predicted to be pathogenic or benign in 79 patients with epilepsy. Pathogenicity predictions were carried out on 52 nonsynonymous mtDNA mutations in 79 patients with epilepsy by using PolyPhen-2, SIFT BLink and PMut analyses. Gray bar, number of variants predicted to be benign; black bar, number of variants predicted to be pathogenic.

Figure 4

Schematic presentation of haplotypes in mtDNA haplogroup U5a1. Red nodes, patients with epilepsy (N = 9); white nodes, Finnish population controls (N = 19); grey nodes, sequences found in HmtDB database (N = 66). Inside the nodes, patients identified by numbers; population controls by numbers C1 - C21 [19], database controls by numbers D1 – D66. Only discriminant variants for the four haplotypes are shown. CRS, the revised Cambridge Reference Sequence [GenBank: NC_012920]. Unless marked otherwise, variants are transitions. GenBank accession for database controls; D1 - D3: AY339528, AY339529, EF657601; D4 – D24: GU296581, GU296583, GU296594, GU296558, HM852852, GU459066, HM852873, DQ489510, GQ160809, GU296652, GU296636, GU296601, GU296595, EU597527, EU698951, GQ368895, GU206811, EU523128, DQ904330, DQ826448, EF657412; D25 - D29: AY339523, DQ112838, EF397754, HM490393, JN604831; D30 - D66: AY339524, AY339525, AY339526, AY339527, EF657616, EF363686, EF177408, EU215455, GU391321, GQ214520, HM246245, HM229344, GU122993, HM144108, HM142902, GU296650, GU296635, GU296634, GU296626, GU296615, GU296613, GU296605, GU296602, GU296597, GU296596, GU296580, GU296574, GU296548, GU797137, EU007851, EU124886, AM260578, AM260577, AM260576, AM260573, AM260572, HM765474.