ClinVar Miner

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

gnomAD frequency: 0.00027  dbSNP: rs150888506
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Total submissions: 13
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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 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 79 of the CPT2 protein (p.Lys79Thr). This variant is present in population databases (rs150888506, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with CPT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 460433). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or 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 Laboratory Services, 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 palmitoyl transferase II deficiency, severe infantile form 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
Revvity Omics, Revvity RCV001571245 SCV003829976 uncertain significance not provided 2023-05-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003403273 SCV004106040 uncertain significance CPT2-related condition 2022-11-10 criteria provided, single submitter clinical testing The CPT2 c.236A>C variant is predicted to result in the amino acid substitution p.Lys79Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.096% of alleles in individuals of Ashkenazi Jewish descent and 0.043% in in individuals of Non-Finnish European descent in gnomAD, including one homozygous individual (http://gnomad.broadinstitute.org/variant/1-53667997-A-C), which may be too common to be an unreported disease-causing variant. Although we suspect that this variant may be benign, at this time its clinical significance is uncertain due to the absence of conclusive functional and genetic evidence.
Genome-Nilou Lab RCV003456089 SCV004179294 uncertain significance Encephalopathy, acute, infection-induced, susceptibility to, 4 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001449651 SCV004179295 uncertain significance Carnitine palmitoyl transferase II deficiency, severe infantile form 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003451159 SCV004179296 uncertain significance Carnitine palmitoyl transferase II deficiency, neonatal form 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003451158 SCV004179297 uncertain significance Carnitine palmitoyl transferase II deficiency, myopathic form 2023-04-11 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV001571245 SCV004229556 uncertain significance not provided 2023-07-07 criteria provided, single submitter clinical testing Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity (http://gnomad.broadinstitute.org). Computational tools predict that this variant is not damaging.
Natera, Inc. RCV000530003 SCV001454115 uncertain significance Carnitine palmitoyltransferase II deficiency 2020-01-27 no assertion criteria provided clinical testing

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