ClinVar Miner

Submissions for variant NM_001352514.2(HLCS):c.1390G>T (p.Val464Leu)

gnomAD frequency: 0.00043  dbSNP: rs144705277
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000478103 SCV000565063 uncertain significance not provided 2017-02-27 criteria provided, single submitter clinical testing The V317L variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The V317L variant is observed in 0.01%-1% alleles from individuals of African background, in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The V317L variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV001405509 SCV001607436 likely benign Holocarboxylase synthetase deficiency 2024-11-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV002526512 SCV003748930 likely benign Inborn genetic diseases 2022-01-07 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Revvity Omics, Revvity RCV001405509 SCV003813236 uncertain significance Holocarboxylase synthetase deficiency 2021-08-19 criteria provided, single submitter clinical testing

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