ClinVar Miner

Submissions for variant NM_001352514.2(HLCS):c.1576C>T (p.Gln526Ter) (rs1393866282)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587858 SCV000696689 pathogenic Holocarboxylase synthetase deficiency 2017-05-04 criteria provided, single submitter clinical testing Variant summary: The c.1135C>T (p.Gln379*) variant in HLCS gene is a nonsense change that results in the loss of the 348 amino acids of the protein (~48%). This change is predicted to cause loss of normal protein function through protein truncation or nonsense-mediated mRNA decay. The variant is absent from in the large control population dataset of ExAC (121402 chrs tested). The variant has been identified in compound heterozygosity with known pathogenic alleles in at least one affected individual with biochemically confirmed dx holocarboxylase synthetase deficiency. Taken together, the variant was classified as Pathogenic.
Counsyl RCV000587858 SCV000798117 likely pathogenic Holocarboxylase synthetase deficiency 2018-02-26 criteria provided, single submitter clinical testing
Invitae RCV000587858 SCV001587509 pathogenic Holocarboxylase synthetase deficiency 2020-09-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln379*) in the HLCS gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of holocarboxylase synthetase deficiency (PMID: 18974016). ClinVar contains an entry for this variant (Variation ID: 495865). Loss-of-function variants in HLCS are known to be pathogenic (PMID: 16134170). For these reasons, this variant has been classified as Pathogenic.

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