ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.152+5G>A

gnomAD frequency: 0.00001  dbSNP: rs1397098803
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001337234 SCV001530827 pathogenic Carnitine palmitoyltransferase II deficiency 2023-09-19 criteria provided, single submitter clinical testing Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. This sequence change falls in intron 1 of the CPT2 gene. It does not directly change the encoded amino acid sequence of the CPT2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has been observed in individual(s) with carnitine palmitoyltransferase II deficiency (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1034501). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001760441 SCV001991948 uncertain significance not provided 2021-11-02 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (Lek et al., 2016); In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 17576681, 9536098, 34158382)
Centogene AG - the Rare Disease Company RCV001810032 SCV002059350 uncertain significance Carnitine palmitoyl transferase II deficiency, severe infantile form 2020-11-04 criteria provided, single submitter clinical testing

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