NM_000098.3(CPT2):c.39_46dup (p.Val16fs) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 18, 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:: RCV001956469.4

Allele description [Variation Report for NM_000098.3(CPT2):c.39_46dup (p.Val16fs)]

NM_000098.3(CPT2):c.39_46dup (p.Val16fs)

Genes:

LOC129930561:ATAC-STARR-seq lymphoblastoid silent region 902 [Gene]
CPT2:carnitine palmitoyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1p32.3

Genomic location:

Preferred name:

NM_000098.3(CPT2):c.39_46dup (p.Val16fs)

HGVS:

NC_000001.11:g.53196982_53196989dup
NG_008035.1:g.5554_5561dup
NM_000098.3:c.39_46dupMANE SELECT
NM_001330589.2:c.39_46dup
NP_000089.1:p.Val16fs
NP_001317518.1:p.Val16fs
NC_000001.10:g.53662651_53662652insGGCCCCGC
NC_000001.10:g.53662654_53662661dup

Protein change:

V16fs

Links:

dbSNP: rs2100254713

NCBI 1000 Genomes Browser:

rs2100254713

Molecular consequence:

NM_000098.3:c.39_46dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330589.2:c.39_46dup - 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

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spermatogenesis-associated serine-rich protein 2 isoform X4 [Homo sapiens]
spermatogenesis-associated serine-rich protein 2 isoform X4 [Homo sapiens]
gi|2462533913|ref|XP_054228970.1|

Protein
PREDICTED: Homo sapiens spermatogenesis associated serine rich 2 (SPATS2), trans...
PREDICTED: Homo sapiens spermatogenesis associated serine rich 2 (SPATS2), transcript variant X6, mRNA
gi|2462533898|ref|XM_054372988.1|

Nucleotide
PREDICTED: Homo sapiens spermatogenesis associated serine rich 2 (SPATS2), trans...
PREDICTED: Homo sapiens spermatogenesis associated serine rich 2 (SPATS2), transcript variant X10, mRNA
gi|2462533902|ref|XM_054372990.1|

Nucleotide
spermatogenesis-associated serine-rich protein 2 isoform X1 [Homo sapiens]
spermatogenesis-associated serine-rich protein 2 isoform X1 [Homo sapiens]
gi|2217290659|ref|XP_047285366.1|

Protein
PREDICTED: Mustela nigripes CD22 molecule (CD22), transcript variant X3, mRNA
PREDICTED: Mustela nigripes CD22 molecule (CD22), transcript variant X3, mRNA
gi|2575396037|ref|XM_059381751.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002245970	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 18, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16781677, 16996287, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002245970

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 18, 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

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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002245970.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1458619). This variant has not been reported in the literature in individuals affected with CPT2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Val16Alafs*60) 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).

#	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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