ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.236A>C (p.Lys79Thr) (rs150888506)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000530003 SCV000632603 uncertain significance Carnitine palmitoyltransferase II deficiency 2019-11-21 criteria provided, single submitter clinical testing This sequence change replaces lysine with threonine at codon 79 of the CPT2 protein (p.Lys79Thr). The lysine residue is moderately conserved and there is a moderate physicochemical difference between lysine and threonine. This variant is present in population databases (rs150888506, ExAC 0.04%). This variant has not been reported in the literature in individuals with CPT2-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV000626610 SCV000747311 uncertain significance Genu valgum; Pes planus; Hyperextensibility of the finger joints; Generalized hypotonia; Myopathic facies; Hyperextensible hand joints; Hyperextensibility at elbow 2017-01-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000530003 SCV001252951 uncertain significance Carnitine palmitoyltransferase II deficiency 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Pars Genome Lab RCV001449651 SCV001652852 uncertain significance Carnitine palmitoyltransferase II deficiency, infantile 2021-05-18 criteria provided, single submitter clinical testing
GeneDx RCV001571245 SCV001795677 uncertain significance not provided 2020-08-21 criteria provided, single submitter clinical testing Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Natera, Inc. RCV000530003 SCV001454115 uncertain significance Carnitine palmitoyltransferase II deficiency 2020-01-27 no assertion criteria provided clinical testing

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