ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.98del (p.Gln33fs) (rs917744011)

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Total submissions: 5
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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 RCV000588722 SCV000695407 pathogenic Carnitine palmitoyltransferase II deficiency 2016-11-23 criteria provided, single submitter clinical testing Variant summary: The c.98delA (p.Gln33Argfs) variant in CPT2 gene is a frameshift change that results in the loss of the 589 amino acids of CPT (~90%). This change is predicted to cause loss of normal protein function through protein truncation or nonsense-mediated mRNA decay. The variant is absent from the large control population dataset of ExAC, but has been reported in at least 1 severely affected individual in compound heterozygosity with a known pathogenic variant (p.S113L) via published report. Taking together, the variant was classified as Pathogenic.
Invitae RCV000588722 SCV001219804 pathogenic Carnitine palmitoyltransferase II deficiency 2020-10-30 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln33Argfs*40) in the CPT2 gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has been observed in individual(s) with clinical features of CPT2 deficiency (PMID: 21913903). ClinVar contains an entry for this variant (Variation ID: 495549). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Loss-of-function variants in CPT2 are known to be pathogenic (PMID: 16781677, 16996287). For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000984252 SCV001132375 likely pathogenic Carnitine palmitoyltransferase II deficiency, infantile 2015-07-28 no assertion criteria provided clinical testing
Natera, Inc. RCV000588722 SCV001461210 pathogenic Carnitine palmitoyltransferase II deficiency 2020-09-16 no assertion criteria provided clinical testing
GeneDx RCV001569307 SCV001793355 pathogenic not provided 2021-07-23 no assertion criteria provided clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016) This variant is associated with the following publications: (PMID: 21913903, 30957255)

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