ClinVar Miner

Submissions for variant NM_002225.5(IVD):c.164A>T (p.Lys55Met) (rs145999491)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000279155 SCV000390857 likely benign Isovaleryl-CoA dehydrogenase deficiency 2018-01-13 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000519068 SCV000617988 uncertain significance not provided 2018-01-18 criteria provided, single submitter clinical testing The K58M variant in the IVD gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The K58M variant is observed in 178/66,740 (0.27%) alleles from individuals of European (non-Finnish) background in the ExAC dataset, and no individuals were reported to be homozgyous (Lek et al., 2016). The K58M variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Lysine are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret K58M as a variant of uncertain significance.
Invitae RCV000279155 SCV001018067 likely benign Isovaleryl-CoA dehydrogenase deficiency 2020-12-08 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV000279155 SCV001367156 uncertain significance Isovaleryl-CoA dehydrogenase deficiency 2018-10-12 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence favors the benign nature of this variant, however the evidence is insufficent to prove its benign nature. The following ACMG criteria were applied in classifying this variant: PP4.
Natera, Inc. RCV000279155 SCV001456702 uncertain significance Isovaleryl-CoA dehydrogenase deficiency 2017-05-27 no assertion criteria provided clinical testing

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