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NM_000098.3(CPT2):c.1535G>A (p.Cys512Tyr) AND Carnitine palmitoyltransferase II deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 2, 2022
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:
RCV001907074.3

Allele description [Variation Report for NM_000098.3(CPT2):c.1535G>A (p.Cys512Tyr)]

NM_000098.3(CPT2):c.1535G>A (p.Cys512Tyr)

Gene:
CPT2:carnitine palmitoyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p32.3
Genomic location:
Preferred name:
NM_000098.3(CPT2):c.1535G>A (p.Cys512Tyr)
HGVS:
  • NC_000001.11:g.53211209G>A
  • NG_008035.1:g.19781G>A
  • NM_000098.2:c.1535G>A
  • NM_000098.3:c.1535G>AMANE SELECT
  • NM_001330589.2:c.1535G>A
  • NP_000089.1:p.Cys512Tyr
  • NP_001317518.1:p.Cys512Tyr
  • NC_000001.10:g.53676881G>A
  • NM_000098.3:c.1535G>A
Protein change:
C512Y
Links:
dbSNP: rs1490239014
NCBI 1000 Genomes Browser:
rs1490239014
Molecular consequence:
  • NM_000098.3:c.1535G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330589.2:c.1535G>A - missense variant - [Sequence Ontology: SO:0001583]

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002182018Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002182018.2

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

Description

This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 512 of the CPT2 protein (p.Cys512Tyr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CPT2-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CPT2 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024