Disorders of Folate Metabolism and Transport Panel

Folate compounds, also known as vitamin B9, play an important role in a number of cellular processes. This includes DNA synthesis, repair, methylation, and other one-carbon transfer reactions (Heales et al. 2016). Deficiency of folate transport or metabolism can lead to global and/or cerebral folate deficiency, which causes a number of clinical symptoms. These symptoms may be hematological (such as megaloblastic anemia), neurological (including, but not limited to, developmental delay, hypotonia, ataxia, spasticity, seizures, intellectual disability, behavioral and psychiatric symptoms) and/or immunological (for example, infection with unusual organisms and even immunological deficiency severe enough to mimic severe combined immune deficiency (SCID)) (Forges et al. 2010; Grapp et al. 2012; Diop-Bove et al. 2014; Watkins and Rosenblatt 2014; Froese et al. 2016). Biochemical analysis may reveal low levels of folate or 5-methyltetrahydrofolate (5-MTHF) in the serum and/or cerebrospinal fluid (Pérez-Dueñas et al. 2010; Diop-Bove et al. 2014). In addition, in some cases hyperhomocysteinemia and homocystinuria may be observed, potentially along with changes in S-adenosylhomocysteine, cystathionine, and/or methionine levels in the plasma (Watkins and Rosenblatt 2014; Froese et al. 2016). Onset of these disorders typically occurs in infancy or early childhood (Forges et al. 2010; Grapp et al. 2012; Diop-Bove et al. 2014).

Three genes known to cause deficiency of folate transport or metabolism (FOLR1, MTHFR and SLC46A1) are included in this test. Pathogenic variants in these genes cause cerebral folate deficiency, severe MTHFR deficiency, or hereditary folate malabsorption, respectively. All of these disorders are autosomal recessive. Pathogenic variants in the MTHFR gene are the most common genetic cause of folate metabolic errors, with over 100 reported causative variants linked to severe MTHFR deficiency in the literature to date. Pathogenic variants in the FOLR1 and SLC46A1 genes are less common, with close to 20 variants reported in each gene. The majority of reported pathogenic variants in these genes are missense, although nonsense, splicing, and small deletions and duplications have all been reported as well (Human Gene Mutation Database).

Please see individual test descriptions for information on the molecular biology of each gene.

To date, nearly all reported MTHFR and SLC46A1 patients have had two pathogenic variants detectable via direct gene sequencing (Goyette et al. 1995; Kluijtmans et al. 1998; Sibani et al. 2000; Sibani et al. 2003; Zhao et al. 2007; Urreizti et al. 2010; Mahadeo et al. 2011; Shin et al. 2011; Diop-Bove et al. 2014; Burda et al. 2015). Based on these studies, a clinical sensitivity of ≥98% is expected for MTHFR and SLC46A1 patients.

FOLR1 was sequenced in 72 patients with low levels (<40nmol/l) of 5MTHF in cerebrospinal fluid. Pathogenic FOLR1 variants were identified in 10 (~14%) patients (Grapp et al. 2012). The authors noted that of the 14 patients that had extremely low CSF 5MTHF levels (<5nmol/l), 10 (~70%) had pathogenic FOLR1 variants.

To date, no large deletions or duplications have been reported in FOLR1 or MTHFR (Human Gene Mutation Database).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes 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 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).

Please note that as recommended by the ACMG, ACOG and AHA, we do not offer testing specifically 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).