Mitochondrial DNA Depletion Syndrome via the FBXL4 Gene

Mitochondrial DNA depletion syndromes are characterized by deficiencies in the maintenance or integrity of the mitochondrial DNA (mtDNA) genome, resulting in a significant decrease in the abundance of mtDNA within the cell (El-Hattab et al. 2013. PubMed ID: 23385875). These diseases, which are caused by pathogenic variants in nuclear-encoded genes, exhibit significant clinical and genetic heterogeneity. To date, four major forms of mtDNA depletion syndrome have been described: myopathic, encephalomyopathic, hepatocerebral, and neurogastrointestinal.

FBXL4-associated mtDNA depletion syndrome manifests as severe encephalopathy (hypotonia, failure to thrive, white matter alterations, and developmental delay) accompanied by lactic acidosis and combined respiratory chain abnormalities (Antoun et al. 2016. PubMed ID: 26404457; Bonnen et al. 2013. PubMed ID: 23993193; Gai et al. 2013. PubMed ID: 23993194; Huemer et al. 2015. PubMed ID: 25868664). Respiratory insufficiency, microcephaly, cerebral atrophy, periventricular or arachnoid cysts, thin corpus callosum, hypertrophic cardiomyopathy, seizures, ataxia, hepatopathy, hearing impairment, dysmorphic features, hyperammonemia, neutropenia, and optic disease (including congenital cataracts and optic atrophy) have also been observed in some affected individuals (Almannai et al. 2017. PubMed ID: 28383868). Onset of this disorder occurs during the neonatal period or in infancy (approximately 3-12 months of age) (Huemer et al. 2015. PubMed ID: 25868664).

Approximately 100 patients have been reported to date with FBXL4-associated mtDNA depletion syndrome. Although a very rare disorder, defects in FBXL4 are one of the more common causes of the encephalomyopathic form of mtDNA depletion syndrome (Dai et al. 2016. PubMed ID: 27743463; El-Hattab et al. 2017. PubMed ID: 28940506).

At this time, there are no effective therapeutic options available for this disorder, and care is supportive. Treatment may include nutritional supplementation, management of symptoms, and routine surveillance of organ systems known to be affected with this disorder. Prognosis is generally poor; there is a high rate of death in childhood (median age of death is ~2 years), although there have been reports of affected individuals surviving into adulthood (Almannai et al. 2017. PubMed ID: 28383868; El-Hattab et al. 2017. PubMed ID: 28940506). At this time, advantages of testing include recurrence risk assessment for reproductive planning.

Pathogenic variants in the nuclear genes FBXL4, SUCLA2, SUCLG1, and RRM2B have been associated with the encephalomyopathic form of mitochondrial DNA (mtDNA) depletion syndrome (Almannai et al. 2017. PubMed ID: 28383868; Bonnen et al. 2013. PubMed ID: 23993193; Gai et al. 2013. PubMed ID: 23993194; Carrozzo et al. 2007. PubMed ID: 17301081; van Hove et al. 2010. PubMed ID: 20453710; Pitceathly et al. 2012. PubMed ID: 23107649). Pathogenic variants in OPA1 may also lead to an encephalomyopathic form of mtDNA depletion, although a limited number of cases have been reported to date (Spiegel et al. 2016. PubMed ID: 26561570).

FBLX4-associated mtDNA depletion syndrome is an autosomal recessive disorder (Gai et al. 2013. PubMed ID: 23993194). The FBXL4 gene, located on chromosome 6q16.1, spans 9 exons and encodes a mitochondrial leucine-rich repeat (LRR)-containing F-box protein essential for mtDNA maintenance, although the precise function of FBXL4 in mitochondria remains undetermined (Bonnen et al. 2013. PubMed ID: 23993193; Gai et al. 2013. PubMed ID: 23993194; Ballout et al. 2019. PubMed ID: 30804983). One study indicates that FBXL4 may function as a regulator of mitochondrial fusion, a process required for remodeling of mitochondrial shape and distribution of mitochondrial contents (Sabouny et al. 2019. PubMed ID: 31442532). Notably, fibroblasts deficient in FBXL4 demonstrate marked mtDNA depletion, mitochondrial fragmentation, reduced mitochondrial inner membrane potential, and severe respiratory chain complex deficiencies (Antoun et al. 2016. PubMed ID: 26404457).

Most of the pathogenic variants documented in FBXL4-associated mtDNA depletion syndrome are either nonsense or missense variants (Antoun et al. 2016. PubMed ID: 26404457; Bonnen et al. 2013. PubMed ID: 23993193; Gai et al. 2013. PubMed ID: 23993194; Huemer et al. 2015. PubMed ID: 25868664). Several splicing variants have also been described, in addition to several small deletions and duplications that create frameshifts and prematurely terminate FBXL4 (Gai et al. 2013. PubMed ID: 23993194; Human Gene Mutation Database). One large deletion of exons 2-4 has been reported (El-Hattab et al. 2017. PubMed ID: 28940506). The contribution of de novo events to disease is unknown; to our knowledge, no de novo variants have been reported to date. Given that this is an autosomal recessive disorder, de novo events are expected to be a rare contributor to disease.

One of the most common causes of FBXL4 appears to be a potential founder variant in individuals of Arab ancestry (c.1698A>G/p.Ile566Met); this particular variant is absent from the gnomAD database, but has been reported in at least sixteen patients to date, often in the homozygous state (Ballout et al. 2019. PubMed ID: 30804983; El-Hattab et al. 2017. PubMed ID: 28940506; Monies et al. 2017. PubMed ID: 28600779). The most prevalent known pathogenic FBXL4 variant in the gnomAD database, a deletion of two nucleotides resulting in premature protein termination (c.1641_1642del/p.Cys547*), has been reported in the Ashkenazi Jewish sub-population at a minor allele frequency of ~0.03% (https://gnomad.broadinstitute.org/variant/6-99323350-TCA-T).

Carriers of FBXL4 pathogenic variants are asymptomatic for mtDNA depletion syndrome (Almannai et al. 2017. PubMed ID: 28383868). To our knowledge, an animal model of disease has not been reported. The OGEE (Online Gene Essentiality) database lists the FBXL4 gene as a nonessential gene for tissue culture (http://ogee.medgenius.info/browse/).

FBXL4 deficiency is a relatively rare cause of general mitochondrial disease; in one cohort of individuals suspected to have a mitochondrial disorder, fewer than 1% (6 out of 808) harbored suspected causative variants in FBXL4 (Dai et al. 2016. PubMed ID: 27743463). However, in a subset of patients who presented with congenital lactic acidosis and a suspected mitochondrial disorder, causative variants in FBXL4 were identified in ~14% of individuals (4 of 28) in the same study.

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

This panel provides full coverage of all coding exons of the FBXL4 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).