NM_000098.3(CPT2):c.1124G>A (p.Gly375Asp) AND Carnitine palmitoyltransferase II deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 21, 2019
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:: RCV000704619.8

Allele description [Variation Report for NM_000098.3(CPT2):c.1124G>A (p.Gly375Asp)]

NM_000098.3(CPT2):c.1124G>A (p.Gly375Asp)

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.1124G>A (p.Gly375Asp)

HGVS:

NC_000001.11:g.53210798G>A
NG_008035.1:g.19370G>A
NM_000098.3:c.1124G>AMANE SELECT
NM_001330589.2:c.1124G>A
NP_000089.1:p.Gly375Asp
NP_001317518.1:p.Gly375Asp
NC_000001.10:g.53676470G>A
NM_000098.2:c.1124G>A

Protein change:

G375D

Links:

dbSNP: rs772843417

NCBI 1000 Genomes Browser:

rs772843417

Molecular consequence:

NM_000098.3:c.1124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330589.2:c.1124G>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

Recent activity

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Mus musculus mediator of RNA polymerase II transcription, subunit 28 homolog (ye...
Mus musculus mediator of RNA polymerase II transcription, subunit 28 homolog (yeast) (Med28), mRNA
gi|31981141|ref|NM_025895.2|

Nucleotide
spermidine/spermine N(1)-acetyltransferase-like protein 1 isoform 2 [Homo sapien...
spermidine/spermine N(1)-acetyltransferase-like protein 1 isoform 2 [Homo sapiens]
gi|1540583188|ref|NP_001354787.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000833575	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 21, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000833575

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 21, 2019)

germline

clinical testing

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

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

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, SCV000833575.6

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

Description

This variant is not present in population databases (ExAC no frequency). 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. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant has not been reported in the literature in individuals with CPT2-related disease. This sequence change replaces glycine with aspartic acid at codon 375 of the CPT2 protein (p.Gly375Asp). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and aspartic acid.

#	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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