Methylmalonic Aciduria and Homocystinuria, cblC type, via the MMACHC 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 cblG. In cblC disorder, two vital cobalamin-dependent cofactors cannot be produced: Adenosyl-cobalamin (AdoCbl) and Methyl-cobalamin (MeCbl). As a result, cblC disorder leads to elevated levels of methylmalonic acid in the blood and urine, as well as hyperhomocysteinemia/homocystinuria. Most patients with cblC disorder are acutely ill during the first month of life and present with microcephaly, feeding difficulties, hypotonia, and lethargy (Carrillo-Carrasco et al. 2013; Fischer et al. 2014; Watkins and Rosenblatt 2014). Affected infants are often small for gestational age, may develop seizures, and become comatose. Many patients have retinopathy and develop systemic pathology, including renal failure, hepatic dysfunction, cardiomyopathy, and/or hemolytic uremic syndrome. Children diagnosed as toddlers may have poor head growth, global developmental delay, seizures, encephalopathy, and cytopenia (including megaloblastic anemia). Although cblC deficiency is considered a pediatric disorder, a small number of affected patients may be diagnosed as teenagers or young adults. Major clinical findings in this late-onset group include confusion, disorientation, gait abnormalities, cognitive decline, and macrocytic anemia (Carrillo-Carrasco et al. 2013; Fischer et al. 2014; Watkins and Rosenblatt 2014).

Autosomal recessive pathogenic variants in the MMACHC gene have been found in patients with cblC disorder. This gene contains four coding exons and is localized to chromosome 1p34.1. While the exact function of the encoded protein remains unknown, it is believed to play a role in Cbl binding and intracellular trafficking. Affected patients appear to have a defect in the reduction of the oxidation state of the central cobalt of cobalamin after it leaves the lysosome. If this reduction does not occur, Cbl cannot be used to form the co-factors AdoCbl and MeCbl and instead leaves the cell (Watkins and Rosenblatt 2014). Over 80 different MMACHC pathogenic variants have been identified, including small insertions and deletions, nonsense variants, splice site variants, and missense variants (Human Gene Mutation Database; Lerner-Ellis et al. 2006; Fischer et al. 2014). Three pathogenic variants have been reported to be the most common (c.271dupA, c.394C>T (p.Arg132*) and c.331C>T (p.Arg111*)) and together account for approximately 50-80% of MMACHC pathogenic alleles (Lerner-Ellis et al. 2006; Fischer et al. 2014). Of these, the c.271dupA is the most common. There does appear to be some genotype-phenotype correlation, with at least one variant (the common p.Arg132* nonsense variant) being associated with late-onset disease (Lerner-Ellis et al. 2009).

In one large study examining 118 patients with confirmed cblC disease, 227 pathogenic variants were identified for an overall sensitivity of ~96% (Lerner-Ellis et al. 2009). Analytical sensitivity is expected to be high because nearly all variants reported in the MMACHC gene to date are detectable via direct sequencing (Human Gene Mutation Database).

Only a single gross deletion has been reported in the MMACHC gene (Weisfeld-Adams and Baker 2015). Therefore, the sensitivity of duplication/deletion testing for this rare disorder, although not precisely known, is low.

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