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NM_001876.4(CPT1A):c.145G>A (p.Gly49Ser) AND Carnitine palmitoyl transferase 1A deficiency

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Jan 25, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV001278073.10

Allele description [Variation Report for NM_001876.4(CPT1A):c.145G>A (p.Gly49Ser)]

NM_001876.4(CPT1A):c.145G>A (p.Gly49Ser)

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.145G>A (p.Gly49Ser)
HGVS:
  • NC_000011.10:g.68812573C>T
  • NG_011801.1:g.34359G>A
  • NM_001031847.3:c.145G>A
  • NM_001876.4:c.145G>AMANE SELECT
  • NP_001027017.1:p.Gly49Ser
  • NP_001867.2:p.Gly49Ser
  • NC_000011.9:g.68580041C>T
Protein change:
G49S
Links:
dbSNP: rs552007692
NCBI 1000 Genomes Browser:
rs552007692
Molecular consequence:
  • NM_001031847.3:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001876.4:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001465066Natera, Inc.
no assertion criteria provided
Uncertain significance
(May 20, 2020)
germlineclinical testing

SCV001786801Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Jul 14, 2021)
germlineclinical testing

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

SCV003296008Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 25, 2024)
germlineclinical testing

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

SCV004046927Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significancegermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

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

Details of each submission

From Natera, Inc., SCV001465066.1

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

From Genome-Nilou Lab, SCV001786801.1

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

From Invitae, SCV003296008.2

#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 Neuberg Centre For Genomic Medicine, NCGM, SCV004046927.1

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

Description

The missense variant c.145G>A (p.Gly49Ser) in CPT1A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has been reported to the ClinVar database as Uncertain Significance. The p.Gly49Ser variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.01600% is reported in gnomAD. The amino acid Gly at position 49 is changed to a Ser changing protein sequence and it might alter its composition and physico-chemical properties. In silico tools predict the variant to be tolerated. The residue is conserved across species. The amino acid change p.Gly49Ser in CPT1A is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. In the absence of another reportable variant the molecular diagnosis is not confirmed.

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

Last Updated: Jun 23, 2024