ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.302C>T (p.Ala101Val)

gnomAD frequency: 0.00675  dbSNP: rs75939866
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001704048 SCV000168036 benign not provided 2018-12-06 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 18550408, 20981092, 16996287)
Labcorp Genetics (formerly Invitae), Labcorp RCV000544913 SCV000632604 benign Carnitine palmitoyltransferase II deficiency 2024-01-31 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000124603 SCV000703977 benign not specified 2017-01-06 criteria provided, single submitter clinical testing
Mendelics RCV000986322 SCV001135291 benign Carnitine palmitoyl transferase II deficiency, severe infantile form 2019-05-28 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000544913 SCV001254824 benign Carnitine palmitoyltransferase II deficiency 2017-04-27 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001704048 SCV001473821 benign not provided 2020-12-17 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000124603 SCV002500718 benign not specified 2022-03-03 criteria provided, single submitter clinical testing Variant summary: CPT2 c.302C>T (p.Ala101Val) results in a non-conservative amino acid change located in the Choline/carnitine acyltransferase domain (IPR039551) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0015 in 251458 control chromosomes, predominantly at a frequency of 0.021 within the African or African-American subpopulation in the gnomAD database, including 3 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 13 fold of the estimated maximal expected allele frequency for a pathogenic variant in CPT2 causing Carnitine Palmitoyltransferase II Deficiency phenotype (0.0016), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Genome-Nilou Lab RCV003456004 SCV004179299 benign Encephalopathy, acute, infection-induced, susceptibility to, 4 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000986322 SCV004179300 benign Carnitine palmitoyl transferase II deficiency, severe infantile form 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003453056 SCV004179301 benign Carnitine palmitoyl transferase II deficiency, neonatal form 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003453055 SCV004179302 benign Carnitine palmitoyl transferase II deficiency, myopathic form 2023-04-11 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001704048 SCV005284612 benign not provided criteria provided, single submitter not provided
Natera, Inc. RCV000544913 SCV001461213 benign Carnitine palmitoyltransferase II deficiency 2020-09-16 no assertion criteria provided clinical testing

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