NM_000098.3(CPT2):c.691C>T (p.Arg231Trp) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 30, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000796802.9

Allele description [Variation Report for NM_000098.3(CPT2):c.691C>T (p.Arg231Trp)]

NM_000098.3(CPT2):c.691C>T (p.Arg231Trp)

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.691C>T (p.Arg231Trp)

HGVS:

NC_000001.11:g.53210365C>T
NG_008035.1:g.18937C>T
NM_000098.3:c.691C>TMANE SELECT
NM_001330589.2:c.691C>T
NP_000089.1:p.Arg231Trp
NP_001317518.1:p.Arg231Trp
NC_000001.10:g.53676037C>T
NM_000098.2:c.691C>T
p.Arg231Trp

Protein change:

R231W

Links:

dbSNP: rs373638740

NCBI 1000 Genomes Browser:

rs373638740

Molecular consequence:

NM_000098.3:c.691C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330589.2:c.691C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Carnitine palmitoyltransferase II deficiency (CPT2)
Synonyms:: Carnitine palmitoyl transferase 2 deficiency; Carnitine palmitoyltransferase deficiency type 2
Identifiers:: MONDO: MONDO:0015515; MedGen: C0342790

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000936330	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 30, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16996287, 24398345, 24602495, 30455135, 28492532
SCV001454230	Natera, Inc.	no assertion criteria provided	Uncertain significance (Sep 16, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000936330

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 30, 2024)

germline

clinical testing

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

SCV001454230

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Sep 16, 2020)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of 16 new disease-causing mutations in the CPT2 gene resulting in carnitine palmitoyltransferase II deficiency.

Isackson PJ, Bennett MJ, Vladutiu GD.

Mol Genet Metab. 2006 Dec;89(4):323-31. Epub 2006 Sep 22.

PubMed [citation]

PMID:: 16996287

Carnitine palmitoyltransferase II (CPT II) deficiency: genotype-phenotype analysis of 50 patients.

Joshi PR, Deschauer M, Zierz S.

J Neurol Sci. 2014 Mar 15;338(1-2):107-11. doi: 10.1016/j.jns.2013.12.026. Epub 2013 Dec 23.

PubMed [citation]

PMID:: 24398345

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000936330.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 231 of the CPT2 protein (p.Arg231Trp). This variant is present in population databases (rs373638740, gnomAD 0.006%). This missense change has been observed in individuals with carnitine palmitoyltransferase II deficiency and/or CPT2-related conditions (PMID: 16996287, 24398345, 24602495, 30455135). ClinVar contains an entry for this variant (Variation ID: 203661). 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%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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 Natera, Inc., SCV001454230.1

#	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

Last Updated: Jan 19, 2025

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