Homocystinuria via the CBS Gene

The transsulfuration pathway involves the interconversion of methionine to homocysteine, and eventually cysteine. This pathway is the main mechanism for removal of methionine (Mudd, Levy and Kraus 2014). The pyridoxine dependent cystathionine β-synthase (CBS) enzyme catalyzes the conversion of homocysteine to cystathionine (Picker and Levy 2014; Mudd, Levy and Kraus 2014). Defects in this enzyme are the most commonly observed cause of homocystinuria without associated methylmalonic aciduria (Picker and Levy 2014; Mudd, Levy and Kraus 2014). Biochemically, patients with this disorder are found to have greatly increased concentrations of plasma and urine homocysteine, total homocysteine, and marked hypermethioninemia (Picker and Levy 2014). This is in contrast to homocystinura caused by defects in the MTR and MTRR genes, which are typically associated with hypomethioninemia (Carrillo-Carrasco et al. 2013; Watkins and Rosenblatt 2014). Clinically, the most common symptoms are developmental delay or intellectual disability, ectopia lentis and/or severe myopia, skeletal abnormalities which can include thinning and lengthening of the long bones as well as osteoporosis, and vascular disease, including potentially fatal thromboembolisms (Kraus et al. 1999; Picker and Levy 2014; Mudd, Levy and Kraus 2014). Other features observed in CBS deficient patients may include psychiatric disturbances, seizures, and extrapyramidal signs (Picker and Levy 2014; Mudd, Levy and Kraus 2014). Age of onset and expressivity of clinical features displayed by patients varies widely, even within sibships, and can range from affected newborns to adults who were previously asymptomatic first presenting with a thromboembolytic event (Carrillo-Carrasco et al. 2013; Picker and Levy 2014; Mudd, Levy and Kraus 2014).

Affected individuals may be identified via newborn screening programs designed to detect hypermethioninemia. However, certain individuals with CBS deficiency may not have increased levels of methionine within the first two to three days of life when newborn screening is performed. Thus, in cases where individuals exhibit clinical symptoms suggestive of CBS deficiency yet had negative newborn screening results, testing for CBS deficiency should still be considered (Picker and Levy 2014).

Treatment includes pyridoxine therapy, to which only about half of affected patients are responsive (Kraus et al. 1999), betaine therapy, folate and vitamin B12 supplementation, and limiting dietary intake of protein and methionine (Picker and Levy 2014). Dietary control is most effective at preventing or ameliorating symptoms when introduced early in life (Mudd, Levy and Kraus 2014).

Classic homocystinuria is inherited in an autosomal recessive manner. The CBS gene is the only gene known to be involved. To date, nearly 200 pathogenic variants have been reported in CBS (Human Gene Mutation Database; CBS Mutation Database). The vast majority of documented variants are missense, although small deletions, insertions and splice variants are also observed. Only a handful of nonsense variants have been reported in this gene to date. In addition, gross deletions have been reported, and the CBS gene is thought to be fairly susceptible to large deletions and rearrangements due to the somewhat high number of Alu repeats at this locus (Mudd, Levy and Kraus 2014). The reported pathogenic variants are found predominantly in the conserved active core of the enzyme, encoded by exons two through seven, with approximately a quarter of missense variants identified to date found in exon three. However, pathogenic variants have been reported in all coding exons of the CBS gene (Mudd, Levy and Kraus 2014; Human Gene Mutation Database).

Three pathogenic variants in the CBS gene are most commonly reported. The first is the missense variant Ile278Thr, which is considered to be a panethnic variant and is thought to account for approximately half of all homocystinuric alleles (Kraus et al. 1999; Mudd, Levy and Kraus 2014). The second is the missense change Gly307Ser, which is the most commonly reported causative variant in patients of Celtic origin and has been reported to account for greater than 70% of alleles in affected individuals of Irish descent (Kraus et al. 1999; Mudd, Levy and Kraus 2014). Lastly, more recent reports have shown that the Thr191Met missense variant makes up approximately 20 - 75% of alleles in individuals of Iberian descent (Urreizti et al. 2006; Cozar et al. 2011).

The CBS protein is part of the transsulfuration pathway in the cell, and is responsible for catalyzing the condensation of serine with homocysteine to form cystathionine, which can then be converted to cysteine. The exact manner in which CBS deficiency leads to the observed clinical symptoms is not fully understood, although a number of possibilities have been proposed (Mudd, Levy and Kraus 2014).

Overall, the sensitivity of this test is expected to be quite high, as most patients reported to date have been found to have two CBS variants detectable via direct sequencing. The majority of studies with larger patient cohorts have reported pathogenic variant detection via direct sequencing in ~95-98% of patient alleles (Gaustadnes et al. 2002; Kruger et al. 2003; Cozar et al. 2011; Karaca et al. 2014).

Large deletions in the CBS gene have been reported, but appear to be a rare cause of disease (Human Gene Mutation Database).

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