ClinVar Miner

Submissions for variant NM_001876.4(CPT1A):c.1163+1G>A (rs148059333)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000548200 SCV000638091 pathogenic Carnitine palmitoyl transferase 1 deficiency 2018-10-16 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 10 of the CPT1A gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Loss-of-function variants in CPT1A are known to be pathogenic. This particular variant has been reported in individuals affected with carnitine palmitoyltransferase 1A deficiency (PMID: 27066452, Invitae). For these reasons, this variant has been classified as Pathogenic.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000548200 SCV000966886 pathogenic Carnitine palmitoyl transferase 1 deficiency 2017-08-07 criteria provided, single submitter clinical testing The c.1163+1G>A (NM_001876.3 c.1163+1G>A) variant in CPT1A has been reported in a compound heterozygous individual with carnitine palmitoyltransferase I (CPT I) deficiency (Choi 2016).This variant has been identified in 0.092% (9/9,828) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database (gnomAD, http:// gnomAD.broadinstitute.org; dbSNP rs148059333). Although this variant has been se en in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Biallelic loss of function of the CPT 1A gene is associated with CPT I deficiency. In summary, the c.1163+1G>A variant meets our criteria to be classified as pathogenic for CPT I deficiency in an au tosomal recessive manner based upon its predicted null effect and occurrence in an affected individual.
Counsyl RCV000410681 SCV000486780 likely pathogenic Carnitine palmitoyltransferase I deficiency 2016-08-04 no assertion criteria provided clinical testing

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