Biallelic variants in HMGCS1 are a novel cause of rare rigid spine syndrome

Rigid spine syndrome is a rare childhood-onset myopathy characterised by slowly progressive or non-progressive scoliosis, neck and spine contractures, hypotonia, and respiratory insufficiency. Biallelic variants in SELENON account for most cases of rigid spine syndrome, however, the underlying genetic cause in some patients remains unexplained. In this study, we used exome and genome sequencing to investigate the genetic basis of rigid spine syndrome in patients without a genetic diagnosis. In five patients from four unrelated families, we identified biallelic variants in HMGCS1 (3-hydroxy-3-methylglutaryl-coenzyme A synthase). These included six missense variants and one frameshift variant distributed throughout HMGCS1. All patients presented with spinal rigidity primarily affecting the cervical and dorsolumbar regions, scoliosis, and respiratory insufficiency. Creatine kinase levels were variably elevated. The clinical course worsened with intercurrent disease or certain drugs in some patients; one patient died from respiratory failure following infection. Muscle biopsies revealed irregularities in oxidative enzyme staining with occasional internal nuclei and rimmed vacuoles. HMGCS1 encodes a key enzyme of the mevalonate pathway, disturbance of which is also associated with HMGCR-limb girdle muscular dystrophy and GGPS1-muscular dystrophy. Quantitative PCR and western blotting confirmed HMGCS1 abundance in skeletal muscle and myogenic precursors. HMGCS1 levels in skeletal muscle were comparable between healthy controls and the index case with a homozygous p.(S447P) substitution. Muscle RNA-seq for a patient with a frameshift variant (c.344_345del:p.S115Wfs*12) and an in trans substitution (p.(Q29L)) showed HMGCS1 transcript levels reduced to 53% compared to controls. The substitution appeared homozygous on RNA-seq, suggesting the allele harbouring the frameshift variant undergoes nonsense mediated decay. hmgcs1-/- zebrafish displayed severe early defects, including immobility at 2 days and death by days 3 post-fertilisation. We anticipate that the variants observed in this cohort have subtle effects on HMGCS1 function given most patients survived to adulthood. In support of the variants being hypomorphic, analyses of recombinant human HMGCS1 protein and four mutants (p.S447P, p.Q29L, p.M70T, p.C268S) showed all mutants maintained their secondary structure and dimerized state and had enzymatic activity comparable to the wildtype. Thermal stability of the mutants was similar or slightly reduced compared to the wildtype. Altogether, our analyses suggest that the identified missense variants in HMGCS1 act through a hypomorphic mechanism yet to be elucidated. Here, we report an additional component of the mevalonate pathway associated with myopathy and suggest biallelic variants in HMGCS1 should be considered in patients presenting with an unresolved rigid spine phenotype.