NM_000152.5(GAA):c.2776T>C (p.Phe926Leu) AND Glycogen storage disease, type II

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 27, 2021
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:: RCV000559302.7

Allele description [Variation Report for NM_000152.5(GAA):c.2776T>C (p.Phe926Leu)]

NM_000152.5(GAA):c.2776T>C (p.Phe926Leu)

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.2776T>C (p.Phe926Leu)

HGVS:

NC_000017.11:g.80118782T>C
NG_009822.1:g.22227T>C
NM_000152.5:c.2776T>CMANE SELECT
NM_001079803.3:c.2776T>C
NM_001079804.3:c.2776T>C
NP_000143.2:p.Phe926Leu
NP_001073271.1:p.Phe926Leu
NP_001073272.1:p.Phe926Leu
LRG_673t1:c.2776T>C
LRG_673:g.22227T>C
NC_000017.10:g.78092581T>C
NM_000152.3:c.2776T>C

Protein change:

F926L

Links:

dbSNP: rs1555603301

NCBI 1000 Genomes Browser:

rs1555603301

Molecular consequence:

NM_000152.5:c.2776T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001079803.3:c.2776T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001079804.3:c.2776T>C - 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

Clear Turn Off Turn On

Russula brevipes strain:BPL707
Russula brevipes strain:BPL707
Russula brevipes BPL707 Standard Draft genome sequencing

BioProject
root metagenome
root metagenome
Metatranscriptome of Pinus contorta CO500 inoculated with Suillus spraguei EM44 root tips from University of Florida, USA - EM44xPcon_wFe_r3

BioProject
LOC101927539 [Homo sapiens]
LOC101927539 [Homo sapiens]
Gene ID:101927539

Gene
101927539[uid] AND (alive[prop]) (1)
Gene
Xanthomonas oryzae pv. oryzae strain JL1 scaffold110, whole genome shotgun seque...
Xanthomonas oryzae pv. oryzae strain JL1 scaffold110, whole genome shotgun sequence
gi|1426333156|ref|NZ_QNLE01000111.1 |WGS:NZ_QNLE01|scaffold110

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000626599	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 27, 2021)	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

SCV000626599

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 27, 2021)

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, SCV000626599.4

#	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 phenylalanine with leucine at codon 926 of the GAA protein (p.Phe926Leu). The phenylalanine residue is moderately conserved and there is a small physicochemical difference between phenylalanine and leucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with GAA-related conditions. ClinVar contains an entry for this variant (Variation ID: 456416). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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

ClinVar

Relating variation to medicine