ClinVar Miner

Submissions for variant NM_001352514.2(HLCS):c.601G>C (p.Glu201Gln)

gnomAD frequency: 0.00008  dbSNP: rs373822815
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000185950 SCV000238907 likely benign not specified 2014-01-18 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV002513956 SCV003275835 uncertain significance Holocarboxylase synthetase deficiency 2024-10-29 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 54 of the HLCS protein (p.Glu54Gln). This variant is present in population databases (rs373822815, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with HLCS-related conditions. ClinVar contains an entry for this variant (Variation ID: 203759). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt HLCS protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV004020253 SCV004882380 uncertain significance Inborn genetic diseases 2022-06-13 criteria provided, single submitter clinical testing The c.160G>C (p.E54Q) alteration is located in exon 5 (coding exon 2) of the HLCS gene. This alteration results from a G to C substitution at nucleotide position 160, causing the glutamic acid (E) at amino acid position 54 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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