SLC33A1-Related Disorders via the SLC33A1 Gene

Huppke-Brendel Syndrome (HBS), also known as congenital cataracts, hearing loss, and neurodegeneration (CCHLND), is a severe progressive autosomal recessive disease that occurs within the first few months of life. Lifespan for affected individuals is approximately 10 months to six years of age. The hallmark features reported in all HBS patients are congenital cataracts, hearing loss, severe developmental delay, low serum copper and ceruloplasmin levels, hypomyelination, cerebellar hypoplasia, and wide subarachnoid spaces (Bindu et al. 2019. PubMed ID: 31194315). Seizures, nystagmus, hypopigmented hair, and hypogenitalism have also been reported in some patients with HBS (Huppke et al. 2012. PubMed ID: 22243965; Chiplunkar et al. 2016. PubMed ID: 27306358). This condition is extremely rare with less than 10 cases reported (Huppke et al. 2012. PubMed ID: 22243965; Chiplunkar et al. 2016. PubMed ID:27306358; Horvath et al. 2005. PubMed ID: 15902551).

Autosomal dominant spastic paraplegia-42 (SPG42) is a condition linked to a specific variant in SLC33A1 (p. Ser113Arg). SPG42 appears to be extremely rare, and was reported in one large Chinese family with 20 out of 57 family members affected. The hallmark features of SPG42 are spastic gait, increased muscle tone, hyperreflexia, and extensor plantar reflexes. The age of onset ranged from 4 years old to 42 years old (Lin et al. 2008. PubMed ID: 19061983). Genetic testing of 220 individuals of European descent with hereditary spastic paraplegias (HSP) did not identify SLC33A1 variants, suggesting that SLC33A1 variants are not a common cause of HSP (Schlipf et al. 2010. PubMed ID: 20461110).

There is no obvious overlap between the HBS and SPG42 phenotypes. Individuals with SPG42 do not show clinical signs of HSP (Mao et al. 2014. PubMed ID: 25402622). Molecular genetic testing is advantageous to establish diagnosis for individuals with HBS or SPG42 and to assist families with reproductive planning.

HBS is inherited as an autosomal recessive disorder that results from homozygous or compound heterozygous pathogenic variants in SLC33A1. To date, six variants (3 missense/nonsense, 1 splicing, and 1 duplication) in SLC33A1 have been reported in patients with HBS (Bindu et al. 2019. PubMed ID: 31194315). These variants have not been reported in population databases. No clinical symptoms of HBS were observed in heterozygous parents of HBS patients (Huppke et al. 2012. PubMed ID: 22243965; Chiplunkar et al. 2016. PubMed ID: 27306358).

SLC33A1 (3q25) encodes the protein, acetyl-CoA transporter 1 (AT-1). AT-1 is located in the membranes of the endoplasmic reticulum and golgi, and functions to transport acetyl CoA into the lumen where it is attached to glycoproteins and gangliosides (O-acetylation) (Kanamori et al. 1997. PubMed ID: 9096318). O-acetylation is an important post-translational modification that helps to target molecules to specific areas where they support proper development and function of tissues (eye and brain) (Argueso et al. 2006. PubMed ID: 16940404; Tapias et al. 2017. PubMed ID: 28161493). Functional studies have shown that changes in SLC33A1 expression lead to a variety of physiological defects. For example, down-regulation of SLC33A1 in cultured cells lead to cell death and autophagy (Jonas et al. 2010. PubMed ID: 20826464). In another example, transgenic mouse models over-expressing human SLC33A1 had widespread neurological defects including increased numbers of dendritic spines and branching and displayed autistic-like behaviors (Hullinger et al. 2016. PubMed ID: 27242167).

Similar to other disorders of copper metabolism (Menkes disease, Wilson disease, and acreuloplasminemia), HBS patients have markedly decreased serum levels of copper and the copper transporting protein, ceruloplasmin (Bindu et al. 2019. PubMed ID: 31194315: Huppke et al. 2012. PubMed ID: 22243965). It has been suggested that ceruloplasmin requires acetylation for secretion and defects in AT-1 lead to decreased levels of ceruloplasmin. To support this, Huppke et al. knocked down AT-1 in HepG2 cells and showed a reduction in ceruloplasmin secretion (Huppke et al. 2012. PubMed ID: 22243965).

SPG42 is an autosomal dominant condition identified in one family and is caused by the SLC33A1 p.Ser113Arg variant. This variant appears to be highly penetrant, with only 1 asymptomatic individual with the variant (Lin et al. 2008. PubMed ID: 19061983). HSPs are a group of clinically and genetically heterogeneous progressive neurodegenerative disorders characterized by lower extremity weakness and spasticity. Approximately 40% of autosomal dominant HSPs are caused by variants in the SPAST gene (Shribman et al. 2019. PubMed ID: 31377012), while variants in ATL1, KIF5A, and REEP1 make up another 20% of HSPs (Schlipf et al. 2010. PubMed ID: 20461110). Studies have demonstrated that the SLC33A1 p.Ser113Arg variant is not a common cause of HSP in European populations (Schlipf et al. 2010. PubMed ID: 20461110).

Several functional studies were conducted to validate the relationship between SLC33A1 p.Ser113Arg and SPG42 originally described by Lin et al. Zebrafish models of knockout SLC33A1 showed phenotypes consistent with other HSP knockout models, having curved-shaped tails with poorly organized motor neurons. This phenotype was rescued by addition of wild-type human SLC33A1 and not rescued by addition of human SLC33A1 p.Ser113Arg (Lin et al. 2008. PubMed ID: 19061983). Studies in heterozygous mouse knock-in model of SLC33A1 p.Ser113Arg showed mice with central neurodegeneration and behavioral abnormalities consistent with HSP phenotypes. Mice homozygous for SLC33A1 p.Ser113Arg were embryonic lethal (Liu et al. 2017. PubMed ID: 27935820). In a separate p.Ser113Arg mouse knock-in study, heterozygous mice displayed additional inflammatory and cancer phenotypes (Peng et al. 2014. PubMed ID: 2482863).

HBS is very rare and shares varying degrees of phenotypic overlap (clinical and biochemical features) with 9 other diseases (Bindu et al. 2019. PubMed ID: 31194315). Sensitivity of this test will be increased when patients are diagnosed by clinical, biochemical, and neuroimaging findings.

To date, at least 72 different spastic gait disease loci and 59 corresponding spastic paraplegia genes (SPGs) have been identified (Shribman et al. 2019. PubMed ID: 31377012). Functional studies of various HSP genes have revealed several cellular pathways that are dysregulated in HSP. It is expected that clinical sensitivity for SPG42 will be low.

Analytical sensitivity should be high as all reported pathogenic variants 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 SLC33A1 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).