NM_000098.3(CPT2):c.1348A>T (p.Arg450Ter) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 2, 2023
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:: RCV001850399.6

Allele description [Variation Report for NM_000098.3(CPT2):c.1348A>T (p.Arg450Ter)]

NM_000098.3(CPT2):c.1348A>T (p.Arg450Ter)

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.1348A>T (p.Arg450Ter)

HGVS:

NC_000001.11:g.53211022A>T
NG_008035.1:g.19594A>T
NM_000098.3:c.1348A>TMANE SELECT
NM_001330589.2:c.1348A>T
NP_000089.1:p.Arg450Ter
NP_001317518.1:p.Arg450Ter
NC_000001.10:g.53676694A>T
NM_000098.2:c.1348A>T

Protein change:

R450*

Links:

dbSNP: rs755395180

NCBI 1000 Genomes Browser:

rs755395180

Molecular consequence:

NM_000098.3:c.1348A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001330589.2:c.1348A>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV002246435	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 2, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16781677, 16996287, 20810031, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002246435

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 2, 2023)

germline

clinical testing

PubMed (4)
[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

Crystal structure of rat carnitine palmitoyltransferase II (CPT-II).

Hsiao YS, Jogl G, Esser V, Tong L.

Biochem Biophys Res Commun. 2006 Aug 4;346(3):974-80. Epub 2006 Jun 9.

PubMed [citation]

PMID:: 16781677
PMCID:: PMC2937350

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

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002246435.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Arg450*) in the CPT2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CPT2 are known to be pathogenic (PMID: 16781677, 16996287). This variant is present in population databases (rs755395180, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with carnitine palmitoyltransferase II deficiency (PMID: 20810031). ClinVar contains an entry for this variant (Variation ID: 188991). For these reasons, this variant has been classified as 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

Last Updated: Sep 29, 2024

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