NM_000098.3(CPT2):c.338C>T (p.Ser113Leu) AND Carnitine palmitoyl transferase II deficiency, myopathic form
- Germline classification:
- Pathogenic/Likely pathogenic (13 submissions)
- Last evaluated:
- Apr 4, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000009510.35
Allele description [Variation Report for NM_000098.3(CPT2):c.338C>T (p.Ser113Leu)]
NM_000098.3(CPT2):c.338C>T (p.Ser113Leu)
- Gene:
- CPT2:carnitine palmitoyltransferase 2 [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 1p32.3
- Genomic location:
- Preferred name:
- NM_000098.3(CPT2):c.338C>T (p.Ser113Leu)
- Other names:
- p.S113L:TCG>TTG
- HGVS:
- NC_000001.11:g.53202427C>T
- NG_008035.1:g.10999C>T
- NM_000098.3:c.338C>TMANE SELECT
- NM_001330589.2:c.338C>T
- NP_000089.1:p.Ser113Leu
- NP_000089.1:p.Ser113Leu
- NP_001317518.1:p.Ser113Leu
- NC_000001.10:g.53668099C>T
- NM_000098.2:c.338C>T
- P23786:p.Ser113Leu
- c.338C>T (p.Ser113Leu)
This HGVS expression did not pass validation- Protein change:
- S113L; SER113LEU
- Links:
- UniProtKB: P23786#VAR_001392; OMIM: 600650.0002; dbSNP: rs74315294
- Molecular consequence:
- NM_000098.3:c.338C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001330589.2:c.338C>T - missense variant - [Sequence Ontology: SO:0001583]
- Observations:
- 5
Condition(s)
- Name:
- Carnitine palmitoyl transferase II deficiency, myopathic form
- Synonyms:
- CARNITINE PALMITOYLTRANSFERASE II DEFICIENCY, ADULT-ONSET; CARNITINE PALMITOYLTRANSFERASE II DEFICIENCY, MYOPATHIC; CPT II DEFICIENCY, MYOPATHIC; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0009704; MedGen: C1833508; Orphanet: 157; Orphanet: 228302; OMIM: 255110
Assertion and evidence details
| Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
|---|---|---|---|---|---|---|
| SCV000029728 | OMIM | no assertion criteria provided | Pathogenic (Jul 1, 1999) | germline | literature only | |
| SCV001448889 | Knight Diagnostic Laboratories, Oregon Health and Sciences University | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (May 3, 2017) | germline | clinical testing | |
| SCV002503776 | Molecular Genetics, Royal Melbourne Hospital
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Aug 27, 2020) | germline | clinical testing | |
| SCV002519438 | Mendelics | criteria provided, single submitter (Mendelics Assertion Criteria 2019) | Pathogenic (May 4, 2022) | germline | clinical testing | |
| SCV002570306 | Johns Hopkins Genomics, Johns Hopkins University | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 9, 2022) | germline | clinical testing | |
| SCV002581870 | MGZ Medical Genetics Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Sep 2, 2022) | germline | clinical testing | |
| SCV002767255 | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (May 6, 2021) | germline | clinical testing | |
| SCV003925086 | New York Genome Center | criteria provided, single submitter (NYGC Assertion Criteria 2020) | Pathogenic (Jun 8, 2022) | germline | clinical testing | |
| SCV004041732 | Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | no assertion criteria provided | Pathogenic (Oct 9, 2023) | germline | clinical testing | |
| SCV004809986 | Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 4, 2024) | germline | clinical testing | |
| SCV005045122 | Clinical Genomics Laboratory, Washington University in St. Louis | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Nov 8, 2023) | germline | clinical testing | |
| SCV006323783 | Clinical Genetics Laboratory, University Hospital Schleswig-Holstein | no assertion criteria provided | Pathogenic (May 28, 2024) | biparental | clinical testing | |
| SCV007540990 | Department of Human Genetics, Hannover Medical School | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Nov 1, 2023) | germline | clinical testing |
Summary from all submissions
| Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
|---|---|---|---|---|---|---|---|---|
| not provided | biparental | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
| not provided | germline | yes | 2 | not provided | not provided | not provided | not provided | clinical testing |
| not provided | germline | unknown | 3 | not provided | not provided | 2 | not provided | clinical testing |
| not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
Citations
PubMed
DiDonato S, Cornelio F, Pacini L, Peluchetti D, Rimoldi M, Spreafico S.
Ann Neurol. 1978 Nov;4(5):465-7.
- PMID:
- 736528
Molecular analysis in Spanish patients with muscle carnitine palmitoyltransferase deficiency.
Martín MA, Rubio JC, De Bustos F, Del Hoyo P, Campos Y, García A, Börnstein B, Cabello A, Arenas J.
Muscle Nerve. 1999 Jul;22(7):941-3.
- PMID:
- 10398215
Details of each submission
From OMIM, SCV000029728.5
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | literature only | PubMed (6) |
Description
In 8 unrelated patients with familial recurrent myoglobinuria due to carnitine palmitoyltransferase II deficiency (255110), Taroni et al. (1993) identified a homozygous 439C-T transition in the CPT2 gene, resulting in a ser133-to-leu substitution (S133L). One of the patients had been reported by DiDonato et al. (1978). Among a total of 25 patients with the disorder, Taroni et al. (1993) found the S113L mutation in 56% of the mutant CPT II alleles and concluded that the S113L missense mutation is the most frequent change found in the myopathic form of CPT II deficiency. One Dutch patient was compound heterozygous for the S113L mutation and the R631C (600650.0001) mutation. In vitro functional expression studies showed that the S113L mutation resulted in normal protein synthesis, but a markedly reduced steady-state level, indicating decreased stability of the mutant protein.
By in vitro functional analysis in fibroblasts, Bonnefont et al. (1996) showed that the S113L mutation resulted in 20% CPT II residual activity with no consequence on long-chain fatty acid (LCFA) oxidation, whereas the Y628S mutation (600650.0005), found in the more severe infantile form of the disorder (600649), resulted in 10% CPT II residual activity and markedly impaired LCFA oxidation. Bonnefont et al. (1996) concluded that CPT II activity must be reduced below a critical threshold for LCFA oxidation in fibroblasts to be impaired. This critical threshold differs among tissues, thus providing a basis for the phenotypic heterogeneity of CPT II deficiency.
In 3 related patients with CPT II deficiency from consanguineous marriages, 2 sibs and a first cousin, Handig et al. (1996) identified homozygosity for the S113L mutation. The cases could be traced back to a common ancestral couple 5 generations earlier. The family showed clinical variability of the disorder.
Martin et al. (1999) identified the S113L mutation in 8 of 14 Spanish patients from 10 unrelated families. Seven patients were homozygous for the mutation, 1 patient was heterozygous, and 6 patients did not carry the mutation on either allele. The mutation was found in the heterozygous state in 7 healthy relatives belonging to 3 different families.
Joshi et al. (2012) reported 2 unrelated patients with stress-induced myopathic carnitine palmitoyltransferase II deficiency who were heterozygous for the S113L mutation. One patient, a 21-year-old female professional tennis player, suffered from exercise-induced attacks of muscle pain, burning sensations, and proximal weakness. The other patient, a 30-year-old male amateur marathon runner, developed muscle cramps and rhabdomyolysis upon extensive exercise and insolation-induced fever.
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Knight Diagnostic Laboratories, Oregon Health and Sciences University, SCV001448889.2
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | 1 | not provided | not provided | not provided | |
From Molecular Genetics, Royal Melbourne Hospital, SCV002503776.2
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (7) |
Description
This sequence change is predicted to replace serine with leucine at codon 113 of the CPT2 protein (p.(Ser113Leu)). The serine residue is highly conserved (100 vertebrates, UCSC), and is located in the mitochondrial matrix region of carnitine O-palmitoyltransferase 2 (UniProt). There is a large physicochemical difference between serine and leucine. The variant is present in a large population cohort at a frequency of 0.14% (rs74315294, 393/282,834 alleles, 4 homozygotes in gnomAD v2.1). The variant is the most commonly occurring pathogenic variant in CPT2 associated with the myopathic form CPT II deficiency (PMID: 20301431). It has been identified in the homozygous state and with a second pathogenic allele in multiple individuals diagnosed with recurrent myoglobinuria/rhabdomyolysis (PM3_VeryStrong; for example PMID: 8358442, 12707442, 20810031). Segregation of the homozygous variant has been reported in at least two families with the phenotype ranging from reduced tolerance to exercise to recurrent rhabdomyolysis (PP1_Strong; PMID: 8786066, 20810031). Homozygous cases are reported with significantly reduced CPT II enzyme activity and slightly reduced or normal long-chain fatty acid oxidation levels in tissues, and markedly reduced CPT II activity is also demonstrated in in vitro expression studies (PP4, PS3_Supporting; PMID: 8358442, 8651281). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (PP3; 6/6 algorithms). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PP1_Strong, PS3_Supporting, PP3, PP4.
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Mendelics, SCV002519438.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Johns Hopkins Genomics, Johns Hopkins University, SCV002570306.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (5) |
Description
This CPT2 variant (rs74315294) has been identified in a large population dataset and the minor allele frequency is neither low enough to consider the variant rare (<0.1%) nor high enough to consider it a population polymorphism (>1%) within the European (non-Finnish) subpopulation (gnomAD: 238/129144 alleles; 0.18%, 1 homozygote). However, the minor allele frequency is low enough to be consistent with a recessive carrier frequency. This variant, c.338C>T (p.Ser113Leu), has been reported in ClinVar, and is the most common pathogenic variant associated with late-onset (myopathic) carnitine palmitoyltransferase deficiency in individuals of European ancestry; most of the patients reported to date were homozygous for this variant. Experimental studies demonstrate that this missense variant significantly reduces enzyme activity. We consider this variant to be pathogenic.
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From MGZ Medical Genetics Center, SCV002581870.2
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | 2 | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | yes | not provided | not provided | not provided | 2 | not provided | not provided | not provided | |
From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767255.2
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (4) |
Description
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with neonatal, infantile and stress-induced myopathic CPT II deficiency. (I) 0106 - This gene is associated with autosomal recessive disease. This gene is generally considered to be associated with an autosomal recessive condition, but some cases of manifesting carriers have been reported for the myopathic form of CPT II deficiency (PMID: 32295037). (I) 0115 - Variants in this gene are known to have variable expressivity. The myopathic form of this condition can manifest from infancy to adulthood and variable onset, frequency, and severity of symptoms have been reported (PMID: 32295037). (I) 0200 - Variant is predicted to result in a missense amino acid change from serine to leucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2) (385 heterozygotes, 4 homozygotes) and is enriched in the Ashkenazi Jewish sub-population. (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated Choline/Carnitine o-acyltransferase domain (NCBI domain). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as the most common cause of the myopathic form of CPT II deficiency in individuals of European ancestry (ClinVar, PMID: 8358442, PMID: 21913903, PMID: 32295037). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From New York Genome Center, SCV003925086.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
| 2 | not provided | 1 | not provided | not provided | clinical testing | not provided |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
| 2 | germline | unknown | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004041732.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre, SCV004809986.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Clinical Genomics Laboratory, Washington University in St. Louis, SCV005045122.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
The CPT2 c.338C>T (p.Ser113Leu) variant is the most common variant in individuals affected with carnintine palmitoyl transferase II deficiency, the mild myopathic form and is reported to segregate with disease. Of those individuals, approximately 18 were compound heterozygous and 38 homozygous. At least 21 heterozygous carriers have also been described with a subset that are clinically symptomatic with muscle CPT activity 39-45% of normal reference (Joshi PR et al., PMID: 23184072; Kaufmann P et al., PMID: 9309694; Taggart RT et al., PMID: 10090476; Taroni F et al., PMID: 8358442). Functional studies show abnormal regulation of the enzyme and thermal instability, indicating that this variant impacts protein function (Taroni F et al., PMID: 8358442; Motlagh L et al., PMID: 26477380). The highest population minor allele frequency in the population database genome aggregation database (v.2.1.1) is 0.75% in the Ashkenazi Jewish population. Computational predictors indicate that the variant is damaging, evidence that correlates with impact to CPT2 function. This variant has been reported in the ClinVar database as a pathogenic variant by 35 submitters and likely pathogenic by 3 submitters. Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic.
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Clinical Genetics Laboratory, University Hospital Schleswig-Holstein, SCV006323783.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | biparental | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
From Department of Human Genetics, Hannover Medical School, SCV007540990.1
| # | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
|---|---|---|---|---|---|---|
| 1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
| # | Sample | Method | Observation | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
| 1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided | |
Last Updated: Jul 6, 2026