NM_000098.3(CPT2):c.353A>G (p.Asp118Gly) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Nov 22, 2023
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:: RCV000440638.22

Allele description [Variation Report for NM_000098.3(CPT2):c.353A>G (p.Asp118Gly)]

NM_000098.3(CPT2):c.353A>G (p.Asp118Gly)

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.353A>G (p.Asp118Gly)

Other names:

p.D118G:GAT>GGT

HGVS:

NC_000001.11:g.53210027A>G
NG_008035.1:g.18599A>G
NM_000098.3:c.353A>GMANE SELECT
NM_001330589.2:c.353A>G
NP_000089.1:p.Asp118Gly
NP_001317518.1:p.Asp118Gly
NC_000001.10:g.53675699A>G
NM_000098.2:c.353A>G

Protein change:

D118G

Links:

dbSNP: rs148035648

NCBI 1000 Genomes Browser:

rs148035648

Molecular consequence:

NM_000098.3:c.353A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330589.2:c.353A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000238787	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Apr 30, 2018)	germline	clinical testing	Citation Link,
SCV000510789	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Oct 25, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000885261	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Uncertain significance (Nov 22, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000238787

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Apr 30, 2018)

germline

clinical testing

Citation Link,

SCV000510789

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Oct 25, 2016)

germline

clinical testing

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

SCV000885261

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Uncertain significance
(Nov 22, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

Details of each submission

From GeneDx, SCV000238787.13

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000510789.1

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

Description

Converted during submission to Uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.001719	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885261.2

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

Description

The CPT2 c.353A>G; p.Asp118Gly variant (rs148035648), to our knowledge, is not reported in the medical literature but is reported as uncertain significance/benign in ClinVar (Variation ID: 203666). This variant is found in the Latino population with an overall allele frequency of 1.5% (505/34418 alleles, including 5 homozygotes) in the Genome Aggregation Database. The aspartic acid at codon 118 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Splicing analyses (Alamut v.2.11) predict that this variant may impact splicing by creating a novel cryptic donor splice site. However, given the lack of clinical and functional data, the significance of the p.Asp118Gly variant is uncertain at this time.

#	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: Oct 20, 2024

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