Homocystinuria, cblE Type, via the MTRR Gene

Cobalamin (Cbl or vitamin B12) is an important cofactor in homocysteine metabolism and in branched-chain amino acid and odd-chain fatty acid catabolism. A series of inherited inborn errors of cobalamin metabolism have been identified, designated cblA through cblJ. In the cblE and cblG disorders, the formation of methionine via methylation of homocysteine is disrupted. Clinically and biochemically, the cblE and cblG disorders are indistinguishable (Watkins and Rosenblatt 2014).

The cblE disorder leads to homocystinuria, hyperhomocystinemia, and hypomethioninemia without methylmalonic aciduria. Clinically, most patients present in childhood with megaloblastic anemia, feeding difficulties, lethargy, hypotonia, cerebral atrophy and developmental delay, though some cases have been reported in which onset occurred during the first months of life or even in adulthood (Palanca et al. 2012; Watkins and Rosenblatt 2014; Zavadáková et al. 2002). Some patients have also exhibited ataxia, cerebral atrophy, neonatal seizures and blindness (Wilson et al 1999). One patient was reported that presented with Haemolytic-Uremic Syndrome as a newborn; bone marrow examination of this patient revealed megalobastic changes and hyperhomocystinemia (Palanca et al. 2012). The cblE disorder can be enzymatically distinguished from the cblG disorder as the activity of methionine synthase from cblG patients is deficient under all conditions tested, whereas the activity of methionine synthase from cblE patients is only deficient under limited reducing conditions (Wilson et al. 1998). Importantly, some cblD variant patients may have a very similar biochemical and clinical profile to cblE and cblG patients. These three disorders are best distinguished by complementation studies or direct gene sequencing (Carrillo-Carrasco et al. 2013).

Some cblE individuals may be identified by newborn screening programs, although this depends on the methods used by the screening laboratory and their ability to detect low levels of methionine. Therefore, complementation analysis and/or molecular genetic testing should still be considered for symptomatic individuals, even if newborn screening results were reported to be normal (Carrillo-Carrasco et al. 2013). A variety of treatment options have been explored for cblG patients, including folinic acid, vitamins B6 and B12, betaine and methionine. However, the outcome of treatment varies with each patient and even with early treatment, no therapy has been found that completely alleviates all symptoms (Carrillo-Carrasco et al. 2013).

Homocystinuria, cblE type is an autosomal recessive disorder, and MTRR is the only gene that is involved. To date, over 25 causative variants have been reported in the MTRR gene (Human Gene Mutation Database). The majority of reported pathogenic variants are missense and small deletions that lead to premature protein termination, although splice variants and small and gross insertions have also been reported. The variants are spread throughout the gene, with no reported mutational hotspots. No predominant variants have been reported, and for the most part, no clear genotype-phenotype correlations have been made. The Ser454Leu variant, however, has been suggested to lead to a milder, predominantly hematological presentation when found in the homozygous state (Vilaseca et al. 2003; Zavadáková et al. 2005).

The cblE disorder is caused by defects in the Methionine Synthase Reductase enzyme, which is responsible for the reductive activation of the Methionine Synthase enzyme. Methionine Synthase catalyzes the methylation of homocysteine, resulting in conversion to methionine. The clinical features of this disorder are thought to be caused by the accumulation of homocysteine and low levels of methionine in the blood as well as the "trapping" of the methyl donor 5-methyltetrahydrofolate (5-MTHF) in the Methionine Synthase enzyme. A lack of adequate levels of methionine leads to a decrease in the cellular level of the critical and widely used methyl group donor S-adenosylmethionine, and "trapping" of 5-MTHF prevents this metabolite from being available for other folate-dependent reactions (Watkins et al. 2002).

Overall, the clinical sensitivity of this test is expected to be relatively high as the majority of confirmed cblE patients identified to date have been found to have MTRR variants that are detectable via DNA sequencing. In one study using cell lines from eight confirmed cblE patients, six patients were found to be compound heterozygous for two MTRR variants, while the other two patients were found to be heterozygous for a single MTRR variant but the second variant was not identified. This suggests an overall detection rate of ~88% (14 out of 16 alleles identified) (Wilson et al. 1999). In a second study of nine confirmed cblE patients, all patients were found to be compound heterozygous or homozygous for variants in the MTRR gene, giving an overall detection rate of 100% (Zavadáková et al. 2005).

It is difficult to estimate the clinical sensitivity of Copy Number Variant detection as to date, only one gross insertion has been reported in the MTRR gene (Wilson et al 1999), and no gross deletions have been reported. However, the clinical sensitivity appears to be relatively low.

This test provides full coverage of all coding exons of the MTRR gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).