Severe MTHFR Deficiency via the MTHFR Gene

Deficiency of the 5,10-methylenetetrahydrofolate reductase (MTHFR deficiency) enzyme is the most commonly observed inborn error of folate metabolism (Kluijtmans et al. 1998; Froese et al. 2016). Patients diagnosed with severe MTHFR deficiency have enzyme activity levels that range from 0 to 20% of normal control levels (Kluijtmans et al. 1998; Sibani et al. 2000). Biochemically, these patients are found to have hyperhomocysteinemia and homocystinuria, elevated plasma S-adenosylhomocysteine and cystathionine, and low to normal levels of methionine in the plasma (Watkins and Rosenblatt 2014; Froese et al. 2016).

Clinically, the onset of symptoms generally occurs in the first two decades of life (Forges et al. 2010). Both neonatal and late-onset patients have been described. Neonatal patients tend to present with general muscular hypotonia, poor feeding and/or failure to thrive, lethargy and microcephaly. These patients may progress rapidly to coma or death via respiratory failure (Forges et al. 2010; Watkins and Rosenblatt 2014; Froese et al. 2016). Patients with late onset MTHFR deficiency generally present later in childhood or early in adulthood with behavioral problems, psychiatric symptoms, cognitive difficulties, progressive encephalopathy, ataxia, spasticity, and sometimes thromboses (Forges et al. 2010; Watkins and Rosenblatt 2014; Froese et al. 2016). Unlike some other disorders of folate metabolism, related methylation disorders and disorders of cobalamin metabolism, MTHFR deficient patients typically do not present with megaloblastic anemia, or methylmalonic aciduria (Watkins and Rosenblatt 2014). Clinical severity is highly variable (Watkins and Rosenblatt 2014).

Early treatment may help ameliorate or prevent symptoms. Although there is not a set treatment regimen for these patients, some combination of betaine and B vitamins (specifically folinic acid, cobalamin, pyridoxine, and riboflavin) has been shown to be helpful for some patients (Burda et al. 2015; Munoz et al. 2015; Froese et al. 2016).

Please note that we do not perform testing for the commonly reported MTHFR C677T and A1298C polymorphisms. See the Testing Strategy section for additional details on this limitation.

MTHFR deficiency is an autosomal recessive disorder, and the MTHFR gene is the only gene that is known to be involved. Over 100 variants have been reported to be associated with severe MTHFR deficiency (Froese et al. 2016; Human Gene Mutation Database). The variants are spread throughout the gene, with pathogenic variants reported in all exons with the exception of the first, non-coding exon. Approximately 70% of the variants are missense, ~25% are splicing or nonsense variants, with the remainder being small deletions, insertions or indels. Interestingly, missense variants are not distributed evenly throughout the gene. The 5’ end of the gene (which encodes the N-terminal catalytic domain) has more than twice the number of reported missense variants as the 3’ end of the gene (Burda et al. 2015; Froese et al. 2016). In general, most reported MTHFR variants are private pathogenic variants, although a few specific variants have been more commonly reported. For example, the c.474A>T (p.Gly158Gly) variant affects MTHFR splicing, and has been reported as a founder mutation in the Bukharian Jewish population (Ben-Shachar et al. 2012). Burda and colleagues (2015) reported the c.1141C>T (p.Arg377Cys) missense variant and c.1530G>A splice variant to be more commonly observed in their cohort.

A genotype-phenotype correlation does appear to exist in severe MTHFR deficient patients. In general, the severity of symptoms and age of onset tend to correlate with the amount of residual enzyme activity in that patient. Lower enzyme activity (particularly below ~1.5% of control levels) is generally associated with an earlier onset and more severe symptoms (Sibani et al. 2000; Forges et al. 2010; Burda et al. 2015).

The MTHFR enzyme catalyzes the NADPH-associated reduction of methylene-tetrahydrofolate (methylene-THF) to methyl-THF. Importantly, methyl-THF is the methyl group donor used in the conversion of homocysteine to methionine (Watkins and Rosenblatt 2014).

The clinical sensitivity of this test is expected to be high, as to date nearly all reported patients have had two pathogenic variants detectable via direct MTHFR sequencing (Goyette et al. 1995; Kluijtmans et al. 1998; Sibani et al. 2000; Sibani et al. 2003; Urreizti et al. 2010; Burda et al. 2015). In these studies, a total of 108 patients were reported with 211 alleles carrying a pathogenic variant, suggesting a clinical sensitivity of ~98%.

To date, no large deletions or duplications have been reported in MTHFR (Human Gene Mutation Database).

This test provides full coverage of all coding exons of the MTHFR gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Sequencing of the MTHFR gene is available only for patients with biochemical and/or clinical features consistent severe MTHFR deficiency, as described above. As recommended by the ACMG, ACOG and AHA, we do not offer testing for the MTHFR common polymorphisms c.665C>T and c.1286A>C (also known as C677T and A1298C) due to the limited clinical utility of such testing (Hickey et al. 2013; Levin and Varga 2016).