U.S. flag

An official website of the United States government

NM_001876.4(CPT1A):c.727C>T (p.Arg243Ter) AND Carnitine palmitoyl transferase 1A deficiency

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Jun 24, 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:
RCV000410747.7

Allele description [Variation Report for NM_001876.4(CPT1A):c.727C>T (p.Arg243Ter)]

NM_001876.4(CPT1A):c.727C>T (p.Arg243Ter)

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.727C>T (p.Arg243Ter)
HGVS:
  • NC_000011.10:g.68796900G>A
  • NG_011801.1:g.50032C>T
  • NM_001031847.3:c.727C>T
  • NM_001876.4:c.727C>TMANE SELECT
  • NP_001027017.1:p.Arg243Ter
  • NP_001867.2:p.Arg243Ter
  • NC_000011.9:g.68564368G>A
  • NM_001876.3:c.727C>T
Protein change:
R243*
Links:
dbSNP: rs779893091
NCBI 1000 Genomes Browser:
rs779893091
Molecular consequence:
  • NM_001031847.3:c.727C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001876.4:c.727C>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

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000485750Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Likely pathogenic
(Feb 8, 2016)
unknownclinical testing

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV001163325Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

SCV002598721Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Sep 28, 2022)
germlineclinical testing

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

Citation Link,

SCV003352727Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jun 24, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Fatty Acid oxidation disorders in a chinese population in taiwan.

Chien YH, Lee NC, Chao MC, Chen LC, Chen LH, Chien CC, Ho HC, Suen JH, Hwu WL.

JIMD Rep. 2013;11:165-72. doi: 10.1007/8904_2013_236. Epub 2013 May 23.

PubMed [citation]
PMID:
23700290
PMCID:
PMC3755561
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000485750.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001163325.1

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002598721.1

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

Description

Variant summary: CPT1A c.727C>T (p.Arg243X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been associated with Carnitine Palmitoyltransferase I Deficiency in HGMD . The variant allele was found at a frequency of 4e-06 in 250902 control chromosomes. c.727C>T has been reported in the literature in one compound heterozygous individual biochemically diagnosed with Carnitine Palmitoyltransferase I Deficiency (Chien_2013). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

From Invitae, SCV003352727.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 370429). This variant has not been reported in the literature in individuals affected with CPT1A-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Arg243*) 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).

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

Last Updated: Feb 28, 2024