ClinVar Miner

Submissions for variant NM_000098.3(CPT2):c.359A>G (p.Tyr120Cys)

gnomAD frequency: 0.00006  dbSNP: rs121918528
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409888 SCV000487481 likely pathogenic Carnitine palmitoyl transferase II deficiency, myopathic form 2016-01-07 criteria provided, single submitter clinical testing
Counsyl RCV000009530 SCV000487482 likely pathogenic Carnitine palmitoyl transferase II deficiency, severe infantile form 2016-01-07 criteria provided, single submitter clinical testing
Counsyl RCV000408956 SCV000487483 likely pathogenic Carnitine palmitoyl transferase II deficiency, neonatal form 2016-01-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000202546 SCV000632607 pathogenic Carnitine palmitoyltransferase II deficiency 2023-12-10 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 120 of the CPT2 protein (p.Tyr120Cys). This variant is present in population databases (rs121918528, gnomAD 0.03%). This missense change has been observed in individual(s) with clinical features of carnitine palmitoyltransferase II deficiency (PMID: 10862092, 16996287, 18550408; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 8968). 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 expected to disrupt CPT2 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects CPT2 function (PMID: 16615913). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000762942 SCV000893365 likely 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 2022-02-16 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV001781212 SCV002023387 likely pathogenic not provided 2021-03-04 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV000409888 SCV002579622 pathogenic Carnitine palmitoyl transferase II deficiency, myopathic form 2021-11-24 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000009530 SCV004179307 likely pathogenic Carnitine palmitoyl transferase II deficiency, severe infantile form 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003473068 SCV004211048 pathogenic Encephalopathy, acute, infection-induced, susceptibility to, 4 2024-03-22 criteria provided, single submitter clinical testing
OMIM RCV000009530 SCV000029748 pathogenic Carnitine palmitoyl transferase II deficiency, severe infantile form 2008-08-01 no assertion criteria provided literature only
GeneReviews RCV000202546 SCV000153657 not provided Carnitine palmitoyltransferase II deficiency no assertion provided literature only
Natera, Inc. RCV000202546 SCV001461215 likely pathogenic Carnitine palmitoyltransferase II deficiency 2020-09-16 no assertion criteria provided clinical testing

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