NM_000098.3(CPT2):c.122C>T (p.Pro41Leu) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 4, 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:: RCV001827488.3

Allele description [Variation Report for NM_000098.3(CPT2):c.122C>T (p.Pro41Leu)]

NM_000098.3(CPT2):c.122C>T (p.Pro41Leu)

Genes:

LOC129930561:ATAC-STARR-seq lymphoblastoid silent region 902 [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.122C>T (p.Pro41Leu)

HGVS:

NC_000001.11:g.53197065C>T
NG_008035.1:g.5637C>T
NM_000098.3:c.122C>TMANE SELECT
NM_001330589.2:c.122C>T
NP_000089.1:p.Pro41Leu
NP_001317518.1:p.Pro41Leu
NC_000001.10:g.53662737C>T
NM_000098.2:c.122C>T

Protein change:

P41L

Links:

dbSNP: rs760976212

NCBI 1000 Genomes Browser:

rs760976212

Molecular consequence:

NM_000098.3:c.122C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330589.2:c.122C>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
SCV002090255	Natera, Inc.	no assertion criteria provided	Uncertain significance (Nov 12, 2020)	germline	clinical testing
SCV003523296	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 4, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22899091, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002090255

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Nov 12, 2020)

germline

clinical testing

SCV003523296

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 4, 2022)

germline

clinical testing

PubMed (2)
[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

Clinical application of massively parallel sequencing in the molecular diagnosis of glycogen storage diseases of genetically heterogeneous origin.

Wang J, Cui H, Lee NC, Hwu WL, Chien YH, Craigen WJ, Wong LJ, Zhang VW.

Genet Med. 2013 Feb;15(2):106-14. doi: 10.1038/gim.2012.104. Epub 2012 Aug 16.

PubMed [citation]

PMID:: 22899091

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Natera, Inc., SCV002090255.1

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003523296.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 41 of the CPT2 protein (p.Pro41Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of autosomal recessive carnitine palmitoyltransferase II (CPTII or CPT2) deficiency (PMID: 22899091). ClinVar contains an entry for this variant (Variation ID: 1200879). 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. 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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