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NM_001876.4(CPT1A):c.298C>T (p.Gln100Ter) AND Carnitine palmitoyl transferase 1A deficiency

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Nov 19, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000009630.13

Allele description [Variation Report for NM_001876.4(CPT1A):c.298C>T (p.Gln100Ter)]

NM_001876.4(CPT1A):c.298C>T (p.Gln100Ter)

Gene:
CPT1A:carnitine palmitoyltransferase 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.3
Genomic location:
Preferred name:
NM_001876.4(CPT1A):c.298C>T (p.Gln100Ter)
HGVS:
  • NC_000011.10:g.68807622G>A
  • NG_011801.1:g.39310C>T
  • NM_001031847.3:c.298C>T
  • NM_001876.4:c.298C>TMANE SELECT
  • NP_001027017.1:p.Gln100Ter
  • NP_001867.2:p.Gln100Ter
  • NC_000011.9:g.68575090G>A
  • NM_001876.3:c.298C>T
  • NP_001867.2:p.Gln100*
Protein change:
Q100*; GLN100TER
Links:
OMIM: 600528.0003; dbSNP: rs80356774
NCBI 1000 Genomes Browser:
rs80356774
Molecular consequence:
  • NM_001031847.3:c.298C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001876.4:c.298C>T - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000029848OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 2002)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000086868GeneReviews
no classification provided
not providedgermlineliterature only

SCV000797175Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Likely pathogenic
(Jan 16, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV002240301Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 19, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

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

Organization of the human liver carnitine palmitoyltransferase 1 gene ( CPT1A) and identification of novel mutations in hypoketotic hypoglycaemia.

Gobin S, Bonnefont JP, Prip-Buus C, Mugnier C, Ferrec M, Demaugre F, Saudubray JM, Rostane H, Djouadi F, Wilcox W, Cederbaum S, Haas R, Nyhan WL, Green A, Gray G, Girard J, Thuillier L.

Hum Genet. 2002 Aug;111(2):179-89. Epub 2002 Jul 16.

PubMed [citation]
PMID:
12189492
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000029848.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a patient with CPT IA deficiency (255120), Gobin et al. (2002) identified a homozygous 298C-T substitution in exon 4 of the CPT1A gene, resulting in a gln100-to-ter (Q100X) mutation. The mutation truncated the protein by 671 amino acids.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000086868.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Counsyl, SCV000797175.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV002240301.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln100*) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with carnitine palmitoyltransferase 1A deficiency (PMID: 12189492). ClinVar contains an entry for this variant (Variation ID: 9063). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024