ClinVar Miner

Submissions for variant NM_001876.4(CPT1A):c.727C>T (p.Arg243Ter)

gnomAD frequency: 0.00001  dbSNP: rs779893091
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410747 SCV000485750 likely pathogenic Carnitine palmitoyl transferase 1A deficiency 2016-02-08 criteria provided, single submitter clinical testing
Baylor Genetics RCV000410747 SCV001163325 likely pathogenic Carnitine palmitoyl transferase 1A deficiency criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000410747 SCV002598721 likely pathogenic Carnitine palmitoyl transferase 1A deficiency 2022-09-28 criteria provided, single submitter clinical testing Variant summary: CPT1A c.727C>T (p.Arg243X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been associated with Carnitine Palmitoyltransferase I Deficiency in HGMD . The variant allele was found at a frequency of 4e-06 in 250902 control chromosomes. c.727C>T has been reported in the literature in one compound heterozygous individual biochemically diagnosed with Carnitine Palmitoyltransferase I Deficiency (Chien_2013). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae RCV000410747 SCV003352727 pathogenic Carnitine palmitoyl transferase 1A deficiency 2023-06-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 370429). This variant has not been reported in the literature in individuals affected with CPT1A-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Arg243*) in the CPT1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CPT1A are known to be pathogenic (PMID: 16169268).

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