Haplotype analysis of the 5,10-methylenetetrahydrofolate reductase (MTHFR) c.1298A>C (E429A) polymorphism

The monomeric enzyme 5,10-methylenetetrahydrofolate reductase (MTHFR, EC 607093, OMIM 236250) catalyzes the reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate (5-MTHF). 5-MTHF is a methyl group donor for the remethylation of homocysteine to methionine. The T-allele of the MTHFR polymorphism c.677C>T (A222V, rs1801133) is associated with reduced MTHFR activity and, thus with an increased total plasma homocysteine level [1]. The frequency of the T-allele of MTHFR c.677C>T differs between ethnic groups and ranges from 6-10% in African countries [2, 3] to more than 17% in Caucasians in North America [1, 4, 5] and more than 50% in Mexican populations [3]. In the literature, the presence of the T-allele has been associated with cardiovascular and cerebrovascular diseases, venous thrombosis, neural tube defects and various cancers [6]. It was hypothesized that this might be due to increased plasma homocysteine levels in carriers of the MTHFR c.677T allele [7]. In addition, the allele's function for DNA synthesis and methylation could be an important factor for the development of such diseases [8]. Previously, we demonstrated that the polymorphism MTHFR c.677C>T (A222V, rs1801133) is associated with a defined MTHFR haplotype in the German population suggesting a founder effect [9]. This result could be confirmed by other groups for other populations [10].

In the present study, we investigated the second functionally relevant MTHFR SNP, the c.1298A>C (E429A, rs1801131) [11]. The derived C-allele of MTHFR c.1298A>C has been found to be associated with decreased MTHFR activity in lymphocytes and cultured human fibroblasts, although this effect was smaller than the effect shown for the T-allele of MTHFR c.677C>T [11–13]. However, the C-allele of the MTHFR c.1298A>C polymorphism could be linked to later onset of neurodegenerative diseases and a lower risk for different types of cancer [12, 14]; [15–18]. Here, we report haplotype data on the c.1298A>C polymorphism in a healthy German population selected by the c.1298A>C genotype suggesting a founder allele in the late ancestry.

The study was approved by the local ethical committee of the University Bonn, Germany, and all individuals gave written informed consent.

In our German population the A- and the C-allele of MTHFR c.1298A>C demonstrated different haplotypes. The most recent common ancestor of these alleles was calculated with approximately 36,600 years. However, analysis of additional populations is required to definitely determine the age of the ancestor allele.

The selection of samples for homozygosity was performed to achieve an easier allocation of haplotypes to the A versus C allele which would have been more difficult in heterozygotes (AC) for MTHFR c.1298A>C. Due to this biased selection, the observed frequencies of the other MTHFR SNPs are not representative for a general population. Nevertheless, this approach was feasible to approximate haplotype frequencies in A versus C alleles of MTHFR c.1298A>C and to estimate the age of the derived allele, c.1298C. Although the DMLE program predicted the most likely age to be approximately 36,600 years according to the major peak, our analysis revealed at least one additional lower peak (Figure 1) that might be artificial or due to the presence of an undefined subpopulation in our study cohort. This as well as the large confidence interval of the estimated age requires replication of our findings in additional samples and other populations.

Our age estimation of the most recent common ancestor of the studied alleles falls into a time period (30,000 to 40,000 years ago, the Aurignacian) which is typically associated with the spread of modern humans (Homo sapiens) in Europe [27, 28]. The frequency of the MTHFR c.1298C allele is significantly higher in central Europe in comparison to African populations [3]. In addition, dietary folate intake can profoundly modify the effect of the C-allele on disease association, and the availability and intake of folate is different in Europe and Africa [29]. In summary, this could indicate an increased frequency of the C-allele due to changes in the (nutritional) environment leading to selective advantages of the C-allele.

Presence of the C-allele has been associated with a later onset of neurodegenerative diseases [12, 14], better fertility (however, only observed for in vitro fertilisation) [30], rarer occurrence of chromosomal aberrations (Down's Syndrome [31]), and lower cancer risk [15–18]. However, adverse effects like an increased risk of neural tube defects [11], hypertension [32] or acute myeloid leukemia in Brazilian children [33] were also described.

Besides historical genetic aspects, the haplotypes presented in this study might be helpful for perinatal diagnosis of MTHFR deficiency based on haplotype analysis in the case of an unknown MTHFR mutation (OMIM 236250). Furthermore, haplotypes might be used for loss of heterozygosity studies comprising chromosome 1p36, which is involved e.g. in glioblastoma formation [34]. In addition, the known linkage disequilibrium of the two MTHFR c.677T and c.1298C alleles [35, 36] was reconfirmed in our study.

The previously described founder effect for the c.677T allele [9] supported by the present data suggests that the MTHFR c.677T and c.1298C alleles arose from two independent ancestral alleles, that both confer a selective advantage.