Creatine Deficiency Syndrome via the SLC6A8 Gene

Creatine transporter (CrT) deficiency is an inborn error of creatine biosynthesis causing cerebral creatine deficiency syndrome (CCDS), which typically has an onset in childhood. The creatine transporter protein is required to move creatine out of the blood and into cells, as well as between different cells following endogenous creatine synthesis (Cheillan and Sedel 2016). Characteristic biochemical findings of CrT deficiency include normal levels of creatine and guanidinoacetate (GAA) in the plasma and urine and a normal GAA/creatinine ratio in the plasma. A finding considered pathognomic for CrT deficiency is a high creatine/creatinine ratio in the urine, although it should be noted that this can be normal in affected females (Mercimek-Mahmutoglu and Salomons 2015; Ardon et al. 2016; Cheillan and Sedel 2016). Direct measurement of total creatine levels in the brain is possible by in vivo proton magnetic resonance spectroscopy (¹H-MRS) (Stromberger et al. 2003). In CrT deficient patients, ¹H-MRS analysis reveals a complete absence or dramatic decrease in the brain creatine peak (Heussinger et al. 2017).

All patients with CrT deficiency present with non-progressive intellectual disability (ID) that can range from mild to severe and is associated with language delays (Cheillan and Sedel 2016). In addition to these patients with non-syndromic ID, other patients present with syndromic ID. Additional findings in the syndromic patients can include seizures, movement disorders, behavior disorders, hypotonia and spasticity, dysmorphic features, gastrointestinal findings, and rarely, cardiac findings (Mercimek-Mahmutoglu and Salomons 2015; Cheillan and Sedel 2016). Treatment of CrT deficient patient with dietary methods has thus far had limited success (Fons et al. 2008). However, clinical trials for pharmaceutical therapy are underway (https://clinicaltrials.gov).

It should be noted that secondary creatine deficiency can be caused by defects in the urea and remethylation cycles as well as by ornithine aminotransferase deficiency (Cheillan and Sedel 2016). If creatine deficiency is suspected based on biochemical tests, but primary cerebral creatine deficiency syndromes are ruled out via genetic and enzyme testing, consideration should be given to these disorders.

CrT deficiency is inherited in an X-linked recessive fashion. The majority of reported patients are male, though affected females have also been reported. Females carrying pathogenic SLC6A8 variants range from asymptomatic to severely affected (Mercimek-Mahmutoglu and Salomons 2015). Approximately 30% of pathogenic variants have been reported to occur de novo, while the rest are maternally inherited (Mercimek-Mahmutoglu and Salomons 2015). To date, over 100 pathogenic variants have been reported in the SLC6A8 gene. The most common types of variants reported are missense and small deletions, though nonsense, splicing, and small insertions and indels have been reported, as well as gross deletions and duplications (Human Gene Mutation Database). No obvious genotype-phenotype correlations have yet been made (Mercimek-Mahmutoglu and Salomons 2015). The most commonly reported pathogenic variants are p.Phe107del, p.Pro544Leu and p.Pro554Leu (van de Kamp et al. 2013; Mercimek-Mahmutoglu and Salomons 2015; SLC6A8 Variant Database).

Creatine is required for the storage and transmission of high energy phosphates (such as ATP) in the muscle and brain (Cheillan and Sedel 2016). Endogenous creatine synthesis occurs via the action of the L-arginine:glycine amidinotransferase (AGAT) and N-guanidinoacetate methyltransferase (GAMT) enzymes. The SLC6A8 gene encodes the creatine transporter protein which is required for the uptake of creatine from the blood into cells. In addition, the creatine transporter is required for the transport of guanidinoacetate (GAA) between cells in organs that do not express both AGAT and GAMT in the same cells. This is particularly true in the brain, and explains why deficiencies in the AGAT, GAMT and SLC6A8 proteins result in a large cerebral creatine deficit (Cheillan and Sedel 2016).

In cohorts of patients with X-linked intellectual disability (XLID), pathogenic variants in SLC6A8 have been reported to account for ~0.6 - 3.3% of cases. In cohorts of patients with generalized intellectual disability (syndromic or non-syndromic ID), pathogenic variants in SLC6A8 have been reported to account for ~1.4% of cases (Mercimek-Mahmutoglu and Salomons 2015).

In one study of patients suspected of a cerebral creatine deficiency syndrome (CCDS) based on clinical features, 26 pathogenic variants were identified in 195 patients, for a sensitivity of ~13.3% (Comeaux et al. 2013). In a retrospective study of 101 male patients with clinical, biochemical, enzymatic and neuroimaging test results consistent with creatine transporter deficiency, all patients carried a pathogenic variant in SLC6A8. In ~96% of these patients, the variant was a small variant detectable via direct sequencing, while the remaining ~4% were found to carry gross deletions (van de Kamp et al. 2013).

This test provides full coverage of all coding exons of the SLC6A8 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

This test also includes coverage for the intronic variants c.1392+24_1393_30del and c.1016+21_1016+54del (Hathaway et al. 2010; Cervera-Acedo et al. 2015).