ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.1767G>A (p.Thr589=)

gnomAD frequency: 0.01032  dbSNP: rs77565483
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000078119 SCV000109957 benign not specified 2013-01-14 criteria provided, single submitter clinical testing
GeneDx RCV000078119 SCV000512765 benign not specified 2015-09-15 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000553368 SCV000632596 benign Carnitine palmitoyltransferase II deficiency 2024-01-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV003656100 SCV001159256 benign not provided 2023-09-21 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000553368 SCV001253050 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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000078119 SCV001361326 benign not specified 2019-05-06 criteria provided, single submitter clinical testing Variant summary: CPT2 c.1767G>A alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0042 in 251482 control chromosomes in the gnomAD database, including 6 homozygotes. The observed variant frequency is approximately 3-folds higher than 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 benign. To our knowledge, no occurrence of c.1767G>A in individuals affected with Carnitine Palmitoyltransferase II Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Fulgent Genetics, Fulgent Genetics RCV002498374 SCV002805025 likely benign Carnitine palmitoyl transferase II deficiency, severe infantile form; Carnitine palmitoyl transferase II deficiency, myopathic form; Carnitine palmitoyl transferase II deficiency, neonatal form; Encephalopathy, acute, infection-induced, susceptibility to, 4 2021-07-24 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003456003 SCV004178297 benign Encephalopathy, acute, infection-induced, susceptibility to, 4 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003453002 SCV004178299 benign Carnitine palmitoyl transferase II deficiency, severe infantile form 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003453004 SCV004178300 benign Carnitine palmitoyl transferase II deficiency, neonatal form 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003453003 SCV004178301 benign Carnitine palmitoyl transferase II deficiency, myopathic form 2023-04-11 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV003656100 SCV005284618 benign not provided criteria provided, single submitter not provided
Natera, Inc. RCV000553368 SCV001454244 benign Carnitine palmitoyltransferase II deficiency 2020-09-16 no assertion criteria provided clinical testing

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