NM_000098.3(CPT2):c.482G>A (p.Arg161Gln) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 17, 2022
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:: RCV002618343.2

Allele description [Variation Report for NM_000098.3(CPT2):c.482G>A (p.Arg161Gln)]

NM_000098.3(CPT2):c.482G>A (p.Arg161Gln)

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.482G>A (p.Arg161Gln)

HGVS:

NC_000001.11:g.53210156G>A
NG_008035.1:g.18728G>A
NM_000098.3:c.482G>AMANE SELECT
NM_001330589.2:c.482G>A
NP_000089.1:p.Arg161Gln
NP_001317518.1:p.Arg161Gln
NC_000001.10:g.53675828G>A

Protein change:

R161Q

Molecular consequence:

NM_000098.3:c.482G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330589.2:c.482G>A - 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
SCV002963347	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 17, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 31770251, 12673791, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002963347

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 17, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Repeated and progressive rhabdomyolysis due to a novel carnitine palmitoyltransferase II gene variant in an adult male: A case report.

Shao L, Liu C, Xu L, Yu R, Li Y, Chen M, He Q.

Medicine (Baltimore). 2019 Nov;98(48):e18143. doi: 10.1097/MD.0000000000018143.

PubMed [citation]

PMID:: 31770251
PMCID:: PMC6890328

Correlation between genotype, metabolic data, and clinical presentation in carnitine palmitoyltransferase 2 (CPT2) deficiency.

Thuillier L, Rostane H, Droin V, Demaugre F, Brivet M, Kadhom N, Prip-Buus C, Gobin S, Saudubray JM, Bonnefont JP.

Hum Mutat. 2003 May;21(5):493-501.

PubMed [citation]

PMID:: 12673791

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002963347.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 161 of the CPT2 protein (p.Arg161Gln). This variant is present in population databases (no rsID available, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of CPT2-related conditions (PMID: 31770251). 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 not expected to disrupt CPT2 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant disrupts the p.Arg161 amino acid residue in CPT2. Other variant(s) that disrupt this residue have been observed in individuals with CPT2-related conditions (PMID: 12673791), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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