NM_000098.3(CPT2):c.1646G>A (p.Gly549Asp) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Jan 11, 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:: RCV000202475.19

Allele description [Variation Report for NM_000098.3(CPT2):c.1646G>A (p.Gly549Asp)]

NM_000098.3(CPT2):c.1646G>A (p.Gly549Asp)

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.1646G>A (p.Gly549Asp)

HGVS:

NC_000001.11:g.53213264G>A
NG_008035.1:g.21836G>A
NM_000098.3:c.1646G>AMANE SELECT
NM_001330589.2:c.1577G>A
NP_000089.1:p.Gly549Asp
NP_000089.1:p.Gly549Asp
NP_001317518.1:p.Gly526Asp
NC_000001.10:g.53678936G>A
NM_000098.2:c.1646G>A
P23786:p.Gly549Asp
c.1646G>A (p.Gly549Asp)

Protein change:

G526D

Links:

UniProtKB: P23786#VAR_007971; dbSNP: rs186044004

NCBI 1000 Genomes Browser:

rs186044004

Molecular consequence:

NM_000098.3:c.1646G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330589.2:c.1577G>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
SCV000153670	GeneReviews	no classification provided	not provided	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV001386080	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 11, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10090476, 16996287, 28492532
SCV002092670	Natera, Inc.	no assertion criteria provided	Uncertain significance (Oct 6, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000153670

GeneReviews

no classification provided

not provided

germline

literature only

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

SCV001386080

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 11, 2024)

germline

clinical testing

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

SCV002092670

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Oct 6, 2021)

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, literature only

Citations

PubMed

Carnitine Palmitoyltransferase II Deficiency..

Wieser T.

2004 Aug 27 [updated 2019 Jan 3]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301431

Novel mutations associated with carnitine palmitoyltransferase II deficiency.

Taggart RT, Smail D, Apolito C, Vladutiu GD.

Hum Mutat. 1999;13(3):210-20.

PubMed [citation]

PMID:: 10090476

See all PubMed Citations (4)

Details of each submission

From GeneReviews, SCV000153670.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001386080.5

#	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 glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 549 of the CPT2 protein (p.Gly549Asp). This variant is present in population databases (rs186044004, gnomAD 0.006%). This missense change has been observed in individual(s) with carnitine palmitoyltransferase II deficiency (PMID: 10090476, 16996287). ClinVar contains an entry for this variant (Variation ID: 130890). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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

From Natera, Inc., SCV002092670.1

#	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: Nov 24, 2024

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