Submission Details

The relationship between HLCS and holocarboxylase synthetase deficiency, a rare, autosomal recessive disorder of biotin metabolism, was evaluated using the ClinGen Clinical Validity Framework as of February 18, 2021. Holocarboxylase synthetase covalently links biotin to the five biotin-dependent carboxylases i.e. propionyl-CoA carboxylase, 3-methylcrotonyl-CoA carboxylase, pyruvate carboxylase, and the mitochondrial and cytosolic acetyl-CoA carboxylases. Holocarboxylase synthetase deficiency therefore results in deficiency activity of these carboxylases, also known as Multiple Carboxylase deficiency (MCD). Patients with holocarboxylase synthetase deficiency usually present in the neonatal period or early infancy with tachypnea, skin rash, feeding problems, hypotonia, seizures, developmental delay, alopecia, and coma. Laboratory findings include metabolic acidosis, lactic acidosis, ketosis, hyperammonemia, and elevated 3-hydroxyisovalerate, 3-methylcrotonylglycine, methylcitrate, 3-hydroxypropionate on urine organic acids analysis. In most patients, the clinical and biochemical findings improve upon treatment with oral biotin, but some patients are only partially biotin-responsive. Deficiency of biotinidase, the enzyme that recycles biotin, also leads to MCD although the onset is usually later. Biallelic variants in HLCS were first reported in individuals with holocarboxylase synthetase deficiency in 1994 (Suzuki et al, PMID 7842009). Since then, over 50 variants have been associated with the condition (https://www.ncbi.nlm.nih.gov/clinvar). The mechanism of disease is loss of function. Evidence supporting this gene-disease relationship includes case-level and experimental data. Ten unique variants (missense, nonsense, frameshift, intronic) from ten probands from seven publications were curated (Aoki et al, 1995, PMID 8541348; Dupuis et al, 1996, PMID 8817339; Sakamoto et al, 1998, PMID 9870216; Sakamoto et al, 2000; PMID 10653324; Morrone et al, 2002, PMID: 12124727; Bailey et al, 2008, PMID 18429047; Van Hove et al, 2008, PMID 18974016). Further evidence is available in the literature but the maximum score for genetic evidence (12 points) has been reached. The gene-disease relationship is also supported by the biochemical function of holocarboxylase synthetase in biotinylation of carboxylases, resulting in multiple carboxylase deficiency, which is consistent with the clinical and biochemical findings in these patients, including a specific pattern of abnormalities noted on analysis urine organic acids (León-Del-Rio et al, 1995, PMID 7753853; León-Del-Rio et al, 2017, PMID 28564555), as well as functional studies in fibroblasts from patients showing deficiency of carboxylase activity due to low biotin incorporation, and low affinity of HCS for biotin (Van Hove et al, 2008, PMID 18974016), and results of studies on purified HCS protein with various missense changes identified in patients, that correlate with clinical response to biotin (Dupuis et al, 1999, PMID 10068510). In summary, HLCS is definitively associated with holocarboxylase synthetase deficiency. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.