NM_000152.5(GAA):c.341A>G (p.Lys114Arg) AND Glycogen storage disease, type II

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 2, 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:: RCV003830826.2

Allele description [Variation Report for NM_000152.5(GAA):c.341A>G (p.Lys114Arg)]

NM_000152.5(GAA):c.341A>G (p.Lys114Arg)

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_000152.5(GAA):c.341A>G (p.Lys114Arg)

HGVS:

NC_000017.11:g.80104927A>G
NG_009822.1:g.8372A>G
NM_000152.5:c.341A>GMANE SELECT
NM_001079803.3:c.341A>G
NM_001079804.3:c.341A>G
NM_001406741.1:c.341A>G
NM_001406742.1:c.341A>G
NP_000143.2:p.Lys114Arg
NP_000143.2:p.Lys114Arg
NP_001073271.1:p.Lys114Arg
NP_001073272.1:p.Lys114Arg
NP_001393670.1:p.Lys114Arg
NP_001393671.1:p.Lys114Arg
LRG_673t1:c.341A>G
LRG_673:g.8372A>G
LRG_673p1:p.Lys114Arg
NC_000017.10:g.78078726A>G
NM_000152.3:c.341A>G

Protein change:

K114R

Molecular consequence:

NM_000152.5:c.341A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001079803.3:c.341A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001079804.3:c.341A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406741.1:c.341A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406742.1:c.341A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glycogen storage disease, type II (GSD2)
Synonyms:: ACID ALPHA-GLUCOSIDASE DEFICIENCY; GLYCOGENOSIS, GENERALIZED, CARDIAC FORM; GSD II; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009290; MedGen: C0017921; Orphanet: 365; OMIM: 232300

Recent activity

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long wavelength sensitive opsin 1 [Xenos vesparum]
long wavelength sensitive opsin 1 [Xenos vesparum]
gi|1135511482|gb|APY20681.1|

Protein
Rhodospirillaceae bacterium PNSBFraternidad_5 16S ribosomal RNA gene, partial se...
Rhodospirillaceae bacterium PNSBFraternidad_5 16S ribosomal RNA gene, partial sequence
gi|1018684910|gb|KU992655.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004635312	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 2, 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

SCV004635312

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 2, 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, SCV004635312.1

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

Description

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. 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 GAA protein function. This variant has not been reported in the literature in individuals affected with GAA-related conditions. 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 sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 114 of the GAA protein (p.Lys114Arg).

#	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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