Homocystinuria, cblG Type, via the MTR 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 cblG disorder leads to homocystinuria, hyperhomocystinemia, and hypomethioninemia without methylmalonic aciduria. Clinically, most patients have presented within the first two years of life with megaloblastic anemia and severe developmental delay. Some patients have also exhibited ataxia, cerebral atrophy, neonatal seizures and blindness (Watkins and Rosenblatt 2014; Wilson et al. 1998). A few cases of adult onset cblG disorder have been reported (Watkins and Rosenblatt 2014; Watkins et al. 2002). The cblG disorder can be enzymatically distinguished from the cblE 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). In most cblG patients, normal accumulation of labeled cobalamin is observed. A few "variant" patients with severe clinical features have been identified; these patients were found to have nearly undetectable methionine synthase activity as well as reduced accumulation of labeled cobalamin (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 cblG 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 (Carrillo-Carrasco et al. 2013). 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.

Homocystinuria, cblG type is an autosomal recessive disorder, and MTR is the only gene that is involved. To date, approximately 20 causative variants have been reported in the MTR 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, small insertions and indels have also been reported. The variants are spread throughout the gene, with no reported mutational hotspots. The most commonly reported variant is Pro1173Leu, and most other pathogenic variants are private (Watkins et al. 2002).

The cblG disorder is caused by defects in the Methionine Synthase enzyme, which is responsible for 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 cblG patients identified to date have been found to have MTR variants that are detectable via DNA sequencing. In the largest study of cblG patients to date, Watkins et al. (2002) studied 24 confirmed cblG patients. Full-gene sequencing was performed on 21 of these patients. Two pathogenic variants were identified in ~71% of the patients and a single variant was identified in the remaining ~29%, for an overall detection rate of ~86% (36 of 42 alleles).

To date, no large deletions or duplications have been described in the MTR gene, although most studies of cblG patients were not reported to include deletion and duplication analysis.

This test provides full coverage of all coding exons of the MTR 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).