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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 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no 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)
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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000029728OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 1999)
germlineliterature only

PubMed (6)
[See all records that cite these PMIDs]

SCV001448889Knight Diagnostic Laboratories, Oregon Health and Sciences University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 3, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002503776Molecular Genetics, Royal Melbourne Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 27, 2020)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV002519438Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Pathogenic
(May 4, 2022)
germlineclinical testing

Citation Link,

SCV002570306Johns Hopkins Genomics, Johns Hopkins University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 9, 2022)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV002581870MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 2, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002767255Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 6, 2021)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV003925086New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Pathogenic
(Jun 8, 2022)
germlineclinical testing

Citation Link,

SCV004041732Zotz-Klimas Genetics Lab, MVZ Zotz Klimas
no assertion criteria provided
Pathogenic
(Oct 9, 2023)
germlineclinical testing

SCV004809986Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 4, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005045122Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Nov 8, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV006323783Clinical Genetics Laboratory, University Hospital Schleswig-Holstein
no assertion criteria provided
Pathogenic
(May 28, 2024)
biparentalclinical testing

SCV007540990Department of Human Genetics, Hannover Medical School
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 1, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedbiparentalyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknown3not providednot provided2not providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Muscle carnitine palmityltransferase deficiency: a case with enzyme deficiency in cultured fibroblasts.

DiDonato S, Cornelio F, Pacini L, Peluchetti D, Rimoldi M, Spreafico S.

Ann Neurol. 1978 Nov;4(5):465-7.

PubMed [citation]
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.

PubMed [citation]
PMID:
10398215
See all PubMed Citations (12)

Details of each submission

From OMIM, SCV000029728.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Knight Diagnostic Laboratories, Oregon Health and Sciences University, SCV001448889.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Molecular Genetics, Royal Melbourne Hospital, SCV002503776.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV002519438.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Johns Hopkins Genomics, Johns Hopkins University, SCV002570306.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From MGZ Medical Genetics Center, SCV002581870.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767255.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From New York Genome Center, SCV003925086.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
2not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided
2germlineunknown1not providednot provided1not providednot providednot provided

From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004041732.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre, SCV004809986.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV005045122.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics Laboratory, University Hospital Schleswig-Holstein, SCV006323783.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1biparentalyesnot providednot providednot providednot providednot providednot providednot provided

From Department of Human Genetics, Hannover Medical School, SCV007540990.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 6, 2026

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