ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.1891C>T (p.Arg631Cys)

gnomAD frequency: 0.00001  dbSNP: rs74315293
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000202472 SCV001214137 pathogenic Carnitine palmitoyltransferase II deficiency 2024-01-09 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 631 of the CPT2 protein (p.Arg631Cys). This variant is present in population databases (rs74315293, gnomAD 0.01%). This missense change has been observed in individual(s) with CPTII deficiency (PMID: 1528846, 15754283, 16996287, 17651973; 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: 8952). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CPT2 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001781211 SCV002019726 pathogenic not provided 2021-02-16 criteria provided, single submitter clinical testing
GeneDx RCV001781211 SCV002513152 pathogenic not provided 2022-04-26 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect (significant reduction of enzyme activity compared to wildtype) (Taroni et al., 1992); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 9600456, 17651973, 22975760, 1528846, 8358442, 20810031, 21913903, 15754283)
Fulgent Genetics, Fulgent Genetics RCV002476950 SCV002791054 pathogenic 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 2021-08-30 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000009508 SCV004178345 pathogenic Carnitine palmitoyl transferase II deficiency, severe infantile form 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003473062 SCV004211049 pathogenic Encephalopathy, acute, infection-induced, susceptibility to, 4 2024-03-11 criteria provided, single submitter clinical testing
OMIM RCV000009508 SCV000029726 pathogenic Carnitine palmitoyl transferase II deficiency, severe infantile form 1993-07-01 no assertion criteria provided literature only
GeneReviews RCV000202472 SCV000153673 not provided Carnitine palmitoyltransferase II deficiency no assertion provided literature only
OMIM RCV000415574 SCV000493924 pathogenic Carnitine palmitoyl transferase II deficiency, myopathic form 1993-07-01 no assertion criteria provided literature only
Natera, Inc. RCV000202472 SCV001454248 pathogenic Carnitine palmitoyltransferase II deficiency 2020-09-16 no assertion criteria provided clinical testing

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