1-53210354-C-T
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_000098.3(CPT2):โc.680C>Tโ(p.Pro227Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (โ โ ). Synonymous variant affecting the same amino acid position (i.e. P227P) has been classified as Likely benign.
Frequency
Consequence
NM_000098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT2 | NM_000098.3 | c.680C>T | p.Pro227Leu | missense_variant | 4/5 | ENST00000371486.4 | NP_000089.1 | |
CPT2 | NM_001330589.2 | c.680C>T | p.Pro227Leu | missense_variant | 4/5 | NP_001317518.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250730Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135604
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727222
GnomAD4 genome AF: 0.000315 AC: 48AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74446
ClinVar
Submissions by phenotype
not provided Pathogenic:4
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 18, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 20, 2020 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21709843, 10090476, 18550408, 25827434, 9758712, 22975760, 12673791) - |
Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Nov 26, 2021 | PP3, PP4, PM3, PS3, PS4_moderate - |
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 08, 2022 | The CPT2 c.680C>T p.Pro227Leu variant (rs74315298) is reported as homozygous or compound heterozygous in the literature in multiple individuals with CPT II deficiency (Boemer 2016, Hissink-Muller 2009, Isackson 2008, Yang 1998). This variant is reported in ClinVar (Variation ID: 8964) and is found in the African population with an allele frequency of 0.1% (25/24906 alleles) in the Genome Aggregation Database. The proline at codon 227 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.985). Based on available information, this variant is considered to be pathogenic. References: Boemer F et al. Diagnostic pitfall in antenatal manifestations of CPT II deficiency. Clin Genet. 2016 Feb;89(2):193-7. PMID: 25827434. Hissink-Muller P et al. Neonatal carnitine palmitoyltransferase II deficiency: failure of treatment despite prolonged survival. BMJ Case Rep. 2009;2009:bcr02.2009.1550.PMID: 21709843; PMCID: PMC3027782. Isackson PJ et a. CPT2 gene mutations resulting in lethal neonatal or severe infantile carnitine palmitoyltransferase II deficiency. Mol Genet Metab. 2008 Aug;94(4):422-427. PMID: 18550408. Yang BZ et al. Identification of four novel mutations in patients with carnitine palmitoyltransferase II (CPT II) deficiency. Mol Genet Metab. 1998 Aug;64(4):229-36. PMID: 9758712. - |
Carnitine palmitoyltransferase II deficiency Pathogenic:3Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 02, 2023 | Variant summary: CPT2 c.680C>T (p.Pro227Leu) results in a non-conservative amino acid change located in the Choline/carnitine acyltransferase domain (IPR039551) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.2e-05 in 250730 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in CPT2 causing Carnitine Palmitoyltransferase II Deficiency (5.2e-05 vs 0.0016), allowing no conclusion about variant significance. c.680C>T has been reported in the literature in multiple individuals affected with Carnitine Palmitoyltransferase II Deficiency (example: Boemer_2016 and Hissink-Muller_2009). These data indicate that the variant is very likely to be associated with disease. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Mar 19, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2025 | This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 227 of the CPT2 protein (p.Pro227Leu). This variant is present in population databases (rs74315298, gnomAD 0.1%). This missense change has been observed in individual(s) with carnitine palmitoyltransferase II deficiency (PMID: 9758712, 18550408, 21709843, 25827434). ClinVar contains an entry for this variant (Variation ID: 8964). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt CPT2 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. - |
Carnitine palmitoyl transferase II deficiency, neonatal form Pathogenic:3
Pathogenic, no assertion criteria provided | clinical testing | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | Oct 11, 2020 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2008 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tรผbingen | Jul 31, 2024 | - - |
Carnitine palmitoyl transferase II deficiency, severe infantile form Pathogenic:3
Likely pathogenic, no assertion criteria provided | clinical testing | Counsyl | Apr 24, 2017 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Dec 22, 2022 | ACMG classification criteria: PM2 supporting, PM3 strong, PP3 supporting - |
Carnitine palmitoyl transferase II deficiency, myopathic form;C1833511:Carnitine palmitoyl transferase II deficiency, severe infantile form;C1833518:Carnitine palmitoyl transferase II deficiency, neonatal form;C3280160:Encephalopathy, acute, infection-induced, susceptibility to, 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 13, 2024 | - - |
Encephalopathy, acute, infection-induced, susceptibility to, 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 27, 2024 | - - |
CPT2-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2024 | The CPT2 c.680C>T variant is predicted to result in the amino acid substitution p.Pro227Leu. This variant has been reported, in the homozygous state or heterozygous state with a second CPT2 variant, in several patients with the neonatal form of carnitine palmitoyltransferase (CPT) II deficiency (Yang et al. 1998. PubMed ID: 9758712; Isackson et al. 2008. PubMed ID: 18550408; Hissink-Muller et al. 2009. PubMed ID: 21709843; Boemer et al. 2016. PubMed ID: 25827434). This variant is reported in 0.10% of alleles in individuals of African descent in gnomAD. This variant is interpreted as pathogenic for recessive disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at