NM_000098.3(CPT2):c.1666_1667del (p.Leu556fs) AND Carnitine palmitoyltransferase II deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 25, 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:: RCV000809583.9

Allele description

NM_000098.3(CPT2):c.1666_1667del (p.Leu556fs)

Gene:

CPT2:carnitine palmitoyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p32.3

Genomic location:

Preferred name:

NM_000098.3(CPT2):c.1666_1667del (p.Leu556fs)

HGVS:

NC_000001.11:g.53213284_53213285del
NG_008035.1:g.21856_21857del
NM_000098.3:c.1666_1667delMANE SELECT
NM_001330589.2:c.1597_1598del
NP_000089.1:p.Leu556fs
NP_001317518.1:p.Leu533fs
NC_000001.10:g.53678956_53678957del
NM_000098.2:c.1666_1667delTT

Protein change:

L533fs

Links:

dbSNP: rs1557719455

NCBI 1000 Genomes Browser:

rs1557719455

Molecular consequence:

NM_000098.3:c.1666_1667del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330589.2:c.1597_1598del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000949739	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 25, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 28871440, 29478820, 17936304, 21913903, 28492532
SCV002092673	Natera, Inc.	no assertion criteria provided	Pathogenic (Dec 28, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000949739

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 25, 2024)

germline

clinical testing

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

SCV002092673

Natera, Inc.

no assertion criteria provided

Pathogenic
(Dec 28, 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

Triheptanoin versus trioctanoin for long-chain fatty acid oxidation disorders: a double blinded, randomized controlled trial.

Gillingham MB, Heitner SB, Martin J, Rose S, Goldstein A, El-Gharbawy AH, Deward S, Lasarev MR, Pollaro J, DeLany JP, Burchill LJ, Goodpaster B, Shoemaker J, Matern D, Harding CO, Vockley J.

J Inherit Metab Dis. 2017 Nov;40(6):831-843. doi: 10.1007/s10545-017-0085-8. Epub 2017 Sep 4.

PubMed [citation]

PMID:: 28871440
PMCID:: PMC6545116

Fluxomic assay-assisted diagnosis orientation in a cohort of 11 patients with myopathic form of CPT2 deficiency.

Fontaine M, Kim I, Dessein AF, Mention-Mulliez K, Dobbelaere D, Douillard C, Sole G, Schiff M, Jaussaud R, Espil-Taris C, Boutron A, Wuyts W, Acquaviva C, Vianey-Saban C, Roland D, Joncquel-Chevalier Curt M, Vamecq J.

Mol Genet Metab. 2018 Apr;123(4):441-448. doi: 10.1016/j.ymgme.2018.02.005. Epub 2018 Feb 12.

PubMed [citation]

PMID:: 29478820

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000949739.4

#	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 creates a premature translational stop signal (p.Leu556Valfs*16) in the CPT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 103 amino acid(s) of the CPT2 protein. This variant is present in population databases (no rsID available, gnomAD 0.002%). This premature translational stop signal has been observed in individuals with carnitine palmitoyltransferase II deficiency (PMID: 28871440, 29478820). ClinVar contains an entry for this variant (Variation ID: 653761). This variant disrupts a region of the CPT2 protein in which other variant(s) (p.Glu645Argfs*5) have been determined to be pathogenic (PMID: 17936304, 21913903). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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

From Natera, Inc., SCV002092673.1

#	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: Aug 4, 2024

ClinVar

Relating variation to medicine