NM_053013.4(ENO3):c.716A>G (p.Lys239Arg) AND Glycogen storage disease due to muscle beta-enolase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 2023
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:: RCV001882215.4

Allele description [Variation Report for NM_053013.4(ENO3):c.716A>G (p.Lys239Arg)]

NM_053013.4(ENO3):c.716A>G (p.Lys239Arg)

Gene:

ENO3:enolase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_053013.4(ENO3):c.716A>G (p.Lys239Arg)

HGVS:

NC_000017.11:g.4955455A>G
NG_012063.2:g.14365A>G
NM_001193503.2:c.587A>G
NM_001374523.1:c.716A>G
NM_001374524.1:c.743A>G
NM_001976.5:c.716A>G
NM_053013.4:c.716A>GMANE SELECT
NP_001180432.1:p.Lys196Arg
NP_001361452.1:p.Lys239Arg
NP_001361453.1:p.Lys248Arg
NP_001967.3:p.Lys239Arg
NP_443739.3:p.Lys239Arg
NC_000017.10:g.4858750A>G

Protein change:

K196R

Links:

dbSNP: rs764872268

NCBI 1000 Genomes Browser:

rs764872268

Molecular consequence:

NM_001193503.2:c.587A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374523.1:c.716A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374524.1:c.743A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001976.5:c.716A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_053013.4:c.716A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glycogen storage disease due to muscle beta-enolase deficiency (GSD13)
Synonyms:: GSD XIII; Glycogen storage disease type 13; Enolase-beta deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013046; MedGen: C2752027; Orphanet: 99849; OMIM: 612932

Recent activity

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RecName: Full=E3 ubiquitin-protein ligase TRIM8; AltName: Full=Glioblastoma-expr...
RecName: Full=E3 ubiquitin-protein ligase TRIM8; AltName: Full=Glioblastoma-expressed RING finger protein; AltName: Full=RING finger protein 27; AltName: Full=RING-type E3 ubiquitin transferase TRIM8; AltName: Full=Tripartite motif-containing protein 8
gi|18202744|sp|Q9BZR9.2|TRIM8_HUMAN

Protein
ORF6N domain-containing protein [Oribacterium asaccharolyticum]
ORF6N domain-containing protein [Oribacterium asaccharolyticum]
gi|2689191178|ref|WP_334290521.1|

Protein
singleCell_spheroid_plate1_E14_S274
singleCell_spheroid_plate1_E14_S274

biosample
singleCell_spheroid_plate1_A4_S168
singleCell_spheroid_plate1_A4_S168

biosample
singleCell_spheroid_plate2_A17_S101
singleCell_spheroid_plate2_A17_S101

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002166327	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2023)	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

SCV002166327

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2023)

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, SCV002166327.3

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

Description

This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 239 of the ENO3 protein (p.Lys239Arg). This variant is present in population databases (rs764872268, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with ENO3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1392570). 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 ENO3 protein function with a negative predictive value of 80%. 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.

#	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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