Total submissions: 5
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Illumina Laboratory Services, |
RCV000334425 | SCV000436040 | uncertain significance | Holocarboxylase synthetase deficiency | 2018-01-12 | criteria provided, single submitter | clinical testing | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. |
| Labcorp Genetics |
RCV000334425 | SCV000835889 | uncertain significance | Holocarboxylase synthetase deficiency | 2022-08-12 | criteria provided, single submitter | clinical testing | This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 664 of the HLCS protein (p.Tyr664Cys). This variant is present in population databases (rs776535574, gnomAD 0.04%). 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: 339957). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HLCS protein function. 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 | RCV002520036 | SCV003650860 | uncertain significance | Inborn genetic diseases | 2022-12-15 | criteria provided, single submitter | clinical testing | The c.1991A>G (p.Y664C) alteration is located in exon 11 (coding exon 8) of the HLCS gene. This alteration results from a A to G substitution at nucleotide position 1991, causing the tyrosine (Y) at amino acid position 664 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. |
| Gene |
RCV004591124 | SCV005078002 | uncertain significance | not provided | 2023-11-15 | criteria provided, single submitter | clinical testing | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge |
| Natera, |
RCV000334425 | SCV001453939 | uncertain significance | Holocarboxylase synthetase deficiency | 2020-01-24 | no assertion criteria provided | clinical testing |