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NM_000152.5(GAA):c.2577G>A (p.Trp859Ter) AND Glycogen storage disease, type II

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 14, 2022
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:
RCV002871829.3

Allele description [Variation Report for NM_000152.5(GAA):c.2577G>A (p.Trp859Ter)]

NM_000152.5(GAA):c.2577G>A (p.Trp859Ter)

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.2577G>A (p.Trp859Ter)
HGVS:
  • NC_000017.11:g.80118288G>A
  • NG_009822.1:g.21733G>A
  • NG_137937.1:g.665G>A
  • NM_000152.5:c.2577G>AMANE SELECT
  • NM_001079803.3:c.2577G>A
  • NM_001079804.3:c.2577G>A
  • NM_001406741.1:c.2577G>A
  • NM_001406742.1:c.2577G>A
  • NP_000143.2:p.Trp859Ter
  • NP_000143.2:p.Trp859Ter
  • NP_001073271.1:p.Trp859Ter
  • NP_001073272.1:p.Trp859Ter
  • NP_001393670.1:p.Trp859Ter
  • NP_001393671.1:p.Trp859Ter
  • LRG_673t1:c.2577G>A
  • LRG_673:g.21733G>A
  • LRG_673p1:p.Trp859Ter
  • NC_000017.10:g.78092087G>A
  • NM_000152.3:c.2577G>A
Protein change:
W859*
Molecular consequence:
  • NM_000152.5:c.2577G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001079803.3:c.2577G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001079804.3:c.2577G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406741.1:c.2577G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001406742.1:c.2577G>A - nonsense - [Sequence Ontology: SO:0001587]

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003232761Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 14, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Update of the Pompe disease mutation database with 107 sequence variants and a format for severity rating.

Kroos M, Pomponio RJ, van Vliet L, Palmer RE, Phipps M, Van der Helm R, Halley D, Reuser A; GAA Database Consortium..

Hum Mutat. 2008 Jun;29(6):E13-26. doi: 10.1002/humu.20745.

PubMed [citation]
PMID:
18425781

Predicting cross-reactive immunological material (CRIM) status in Pompe disease using GAA mutations: lessons learned from 10 years of clinical laboratory testing experience.

Bali DS, Goldstein JL, Banugaria S, Dai J, Mackey J, Rehder C, Kishnani PS.

Am J Med Genet C Semin Med Genet. 2012 Feb 15;160C(1):40-9. doi: 10.1002/ajmg.c.31319. Epub 2012 Jan 17.

PubMed [citation]
PMID:
22252923
PMCID:
PMC3278076
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003232761.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. 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 creates a premature translational stop signal (p.Trp859*) in the GAA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GAA are known to be pathogenic (PMID: 18425781, 22252923).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024