Fucosidosis via the FUCA1 Gene

Lysosomal storage disorders are inborn errors of metabolism that result in the gradual accumulation of substrate inside the lysosome, which ultimately leads to cell death. Individually, lysosomal storage disorders are rare, but collectively are estimated to affect 1 in 5,000 live births (Platt et al. 2018. PubMed ID: 30275475). These disorders often present in infancy or early childhood with progressive neurodegeneration accompanied by visceromegaly, but have distinct biochemical findings (Platt et al. 2018. PubMed ID: 30275475).

Fucosidosis is an extremely rare lysosomal storage disorder that arises due to deficient activity of a lysosomal enzyme, α-1-fucosidase, which leads to the gradual accumulation of fucosylated glycolipids, glycoproteins, and oligosaccharides throughout the body (Willems et al. 1999. PubMed ID: 10094192). It affects diverse ethnic groups, with less than 150 reported cases worldwide, and its prevalence is estimated at <1 in 1,000,000. Higher occurrences of fucosidosis have been reported in Italy and the southwestern United States (Willems et al. 1999. PubMed ID: 10094192), Tunisia (Ben Turkia et al. 2008. PubMed ID: 18651239), and Cuba (Menéndez-Sainz et al. 2012. PubMed ID: 22911605). Major clinical features include developmental regression, severe global developmental delay, muscle stiffness, coarse facies, recurrent respiratory infections, abnormal bone development, and dermatological abnormalities (Willems et al. 1991. PubMed ID: 2012122). Less common clinical features of fucosidosis may include visceromegaly and seizures (Willems et al. 1991. PubMed ID: 2012122). The clinical presentation of fucosidosis ranges in severity, with up to 60% of patients dying prior to age 10 secondary to recurrent pulmonary infections or neurological deterioration (Ben Turkia et al. 2008. PubMed ID: 18651239). In spite of phenotypic heterogeneity, the unifying feature of fucosidosis is extremely low α-1-fucosidase enzyme activity in peripheral blood leukocytes, at <5-10% of normal activity levels (Willems et al. 1999. PubMed ID: 10094192).

Some studies suggest that early intervention with bone marrow transplant, hematopoietic stem cell transplantation, or umbilical cord blood transplantation, may improve the outcome of patients diagnosed with fucosidosis prior to significant central nervous system manifestations (Miano et al. 2001. PubMed ID: 11360116, Jiang et al. 2017. PubMed ID: 28238202). Patients and their families may also benefit from a molecular diagnosis for prognostic information, symptom management, and reproductive planning.

The majority of pathogenic variants in FUCA1 are biallelic loss-of-function variants in a compound heterozygous or homozygous state, consistent with autosomal recessive inheritance (Willems et al. 1999. PubMed ID: 10094192; Human Gene Mutation Database). A variety of pathogenic variants have been reported throughout every exon of the FUCA1 gene, with approximately 20% of known variants being missense, and approximately 80% of variants predicted to result in loss-of-function. The known loss-of-function variants include nonsense variants, frame-shift variants, deletions including intragenic and full-gene, as well as splice site variants (Willems et al. 1999. PubMed ID: 10094192; Human Gene Mutation Database). All causative variants disrupt the open-reading frame of FUCA1 rather than the regulatory region, and result in nearly absent enzymatic activity due to destabilization and rapid degradation of mutant α-1-fucosidase in the cell (Willems et al. 1988. PubMed ID: 2903668, Cragg et al. 1997. PubMed ID: 9039984).

Most of the variants reported as causative for fucosidosis are private. While some recurrent variants have been identified in populations where higher incidences of fucosidosis occur, it is not clear whether this is due to a founder effect or intensive fucosidosis screening efforts carried out in those regions (Willems et al. 1999. PubMed ID: 10094192, Ben Turkia et al. 2008. PubMed ID: 18651239, Menéndez-Sainz et al. 2012. PubMed ID: 22911605). The most commonly occurring known pathogenic variant in FUCA1 is a nonsense variant designated c.393T>A (p.Tyr131Term), which has been reported in up to ~0.02% of alleles in a subpopulation in the gnomAD public population database (https://gnomad.broadinstitute.org/variant/1-24192112-A-T) and has been reported in only two patients with fucosidosis to date (Ip et al. 2002. PubMed ID: 12408193; Lin et al. 2007. PubMed ID: 17427030).

FUCA1 encodes α-1-fucosidase, a lysosomal enzyme that catalyzes the removal of terminal sugar moieties called fucose that are commonly present in glycolipids, glycoproteins, and oligosaccharides in cells throughout the body (Willems et al. 1999. PubMed ID: 10094192, Schneider et al. 2017. PubMed ID: 28430973). In the absence of α-1-fucosidase activity, fucosylated molecules progressively accumulate in the lysosome.

Alpha-1-fucosidase contains a 31 amino acid N-terminal signal peptide which targets the protein to the lysosome after synthesis in the ER (AA 1-31), a catalytic glycoside hydrolase domain (AA 35-370), and a non-catalytic C-terminal domain (AA 372-463). All FUCA1 variants reported to date occur within the mature α-1-fucosidase polypeptide, as no documented variants occur within the first 31 amino acids (Willems et al. 1999. PubMed ID: 10094192; Human Gene Mutation Database).

FUCA1 has been cited as a nonessential gene for growth of human tissue culture cells (Online Gene Essentiality, ogee.medgenius.info). Human immortalized keratinocyte cell lines are viable upon siRNA knock-down of FUCA1, suggesting that cells tolerate loss of FUCA1 in cell culture (Valero-Rubio et al. 2018. PubMed ID: 29518279). Importantly, homozygous Fuca1 knock-out mice which completely lack α-1-fucosidase enzyme activity exhibit progressive neurological dysfunction which parallels patients with fucosidosis (Wolf et al. 2016. PubMed ID: 27491075, Stroobants et al. 2018. PubMed ID: 29706874). A canine fucosidosis model which harbors a homozygous 14bp deletion resulting in a frame-shift and premature protein termination at the 3’ end of exon 1 in Fuca1, also closely resembles human fucosidosis (Skelly et al. 1996. PubMed ID: 8730282). Affected canines, like humans, present with <5% α-1-fucosidase enzyme activity compared to controls as well as progressive ataxia, tremor, inability to swallow, wasting, blindness, and deafness (Abraham et al. 1984. PubMed ID: 6477509). The canine model of fucosidosis has recently been used to investigate enzyme replacement therapy (Kondagari et al. 2015. PubMed ID: 26537923).

Clinical sensitivity is difficult to estimate because only a small number of patients with fucosidosis have been reported. Because biallelic pathogenic variants in FUCA1 have been detected in nearly all patients with fucosidosis reported in the literature, we expect clinical sensitivity to be high in patients that have undergone biochemical testing to confirm low α-1-fucosidase enzyme activity. As clinical features of fucosidosis may overlap with other lysosomal storage disorders or hereditary causes of developmental delay, we expect clinical sensitivity to be lower for patients who have not undergone biochemical testing. Analytical sensitivity should be high because all pathogenic variants in FUCA1 reported to date are detectable by sequencing.

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

This test provides full coverage of all coding exons of the FUCA1 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).