NM_001876.4(CPT1A):c.1039dup (p.Leu347fs) AND Carnitine palmitoyl transferase 1A deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 10, 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:: RCV003752498.2

Allele description [Variation Report for NM_001876.4(CPT1A):c.1039dup (p.Leu347fs)]

NM_001876.4(CPT1A):c.1039dup (p.Leu347fs)

Gene:

CPT1A:carnitine palmitoyltransferase 1A [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11q13.3

Genomic location:

Preferred name:

NM_001876.4(CPT1A):c.1039dup (p.Leu347fs)

HGVS:

NC_000011.10:g.68784939dup
NG_011801.1:g.61993dup
NG_011801.2:g.64338dup
NM_001031847.3:c.1039dup
NM_001876.4:c.1039dupMANE SELECT
NP_001027017.1:p.Leu347fs
NP_001867.2:p.Leu347fs
NC_000011.9:g.68552406_68552407insG
NC_000011.9:g.68552407dup

Protein change:

L347fs

Molecular consequence:

NM_001031847.3:c.1039dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001876.4:c.1039dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Carnitine palmitoyl transferase 1A deficiency
Synonyms:: Carnitine palmitoyl transferase 1 deficiency; Carnitine palmitoyltransferase 1A deficiency; CPT1A deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009705; MedGen: C1829703; Orphanet: 156; OMIM: 255120

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Homo sapiens chromosome 16 clone RP11-1348G14, complete sequence
Homo sapiens chromosome 16 clone RP11-1348G14, complete sequence
gi|40018652|gnl|jgi|RP11-1348G14|gb 5285.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004463394	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 10, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16169268, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004463394

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 10, 2023)

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

Homozygous carnitine palmitoyltransferase 1a (liver isoform) deficiency is lethal in the mouse.

Nyman LR, Cox KB, Hoppel CL, Kerner J, Barnoski BL, Hamm DA, Tian L, Schoeb TR, Wood PA.

Mol Genet Metab. 2005 Sep-Oct;86(1-2):179-87.

PubMed [citation]

PMID:: 16169268

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004463394.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CPT1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu347Profs*4) in the CPT1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CPT1A are known to be pathogenic (PMID: 16169268).

#	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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