NM_000098.3(CPT2):c.1767del (p.Ser590fs) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 11, 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:: RCV001855592.3

Allele description [Variation Report for NM_000098.3(CPT2):c.1767del (p.Ser590fs)]

NM_000098.3(CPT2):c.1767del (p.Ser590fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p32.3

Genomic location:

Preferred name:

NM_000098.3(CPT2):c.1767del (p.Ser590fs)

HGVS:

NC_000001.11:g.53213385del
NG_008035.1:g.21957del
NM_000098.3:c.1767delMANE SELECT
NM_001330589.2:c.1698del
NP_000089.1:p.Ser590fs
NP_001317518.1:p.Ser567fs
NC_000001.10:g.53679057del
NM_000098.2:c.1767delG

Protein change:

S567fs

Links:

dbSNP: rs1553169973

NCBI 1000 Genomes Browser:

rs1553169973

Molecular consequence:

NM_000098.3:c.1767del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330589.2:c.1698del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002234476	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 11, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17936304, 21913903, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002234476

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 11, 2023)

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

Clinical features and new molecular findings in Carnitine Palmitoyltransferase II (CPT II) deficiency.

Corti S, Bordoni A, Ronchi D, Musumeci O, Aguennouz M, Toscano A, Lamperti C, Bresolin N, Comi GP.

J Neurol Sci. 2008 Mar 15;266(1-2):97-103. Epub 2007 Oct 23.

PubMed [citation]

PMID:: 17936304

Allelic and phenotypic heterogeneity in 49 Italian patients with the muscle form of CPT-II deficiency.

Fanin M, Anichini A, Cassandrini D, Fiorillo C, Scapolan S, Minetti C, Cassanello M, Donati MA, Siciliano G, D'Amico A, Lilliu F, Bruno C, Angelini C.

Clin Genet. 2012 Sep;82(3):232-9. doi: 10.1111/j.1399-0004.2011.01786.x. Epub 2011 Oct 12.

PubMed [citation]

PMID:: 21913903

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002234476.3

#	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 creates a premature translational stop signal (p.Ser590Alafs*3) in the CPT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 69 amino acid(s) of the CPT2 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CPT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 557080). 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

Last Updated: Feb 28, 2024

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