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NM_000152.5(GAA):c.2741delinsCAG (p.Gln914fs) AND Glycogen storage disease, type II

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Feb 4, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV003610681.3

Allele description [Variation Report for NM_000152.5(GAA):c.2741delinsCAG (p.Gln914fs)]

NM_000152.5(GAA):c.2741delinsCAG (p.Gln914fs)

Gene:
GAA:alpha glucosidase [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_000152.5(GAA):c.2741delinsCAG (p.Gln914fs)
HGVS:
  • NC_000017.11:g.80118747delinsCAG
  • NG_009822.1:g.22192delinsCAG
  • NM_000152.5:c.2741delinsCAGMANE SELECT
  • NM_001079803.3:c.2741delinsCAG
  • NM_001079804.3:c.2741delinsCAG
  • NM_001406741.1:c.2741delinsCAG
  • NM_001406742.1:c.2741delinsCAG
  • NP_000143.2:p.Gln914Profs
  • NP_000143.2:p.Gln914fs
  • NP_001073271.1:p.Gln914fs
  • NP_001073272.1:p.Gln914fs
  • NP_001393670.1:p.Gln914fs
  • NP_001393671.1:p.Gln914fs
  • LRG_673t1:c.2741delAinsCAG
  • LRG_673:g.22192delinsCAG
  • LRG_673p1:p.Gln914Profs
  • NC_000017.10:g.78092546delinsCAG
  • NM_000152.3:c.2741delAinsCAG
Protein change:
Q914fs
Molecular consequence:
  • NM_000152.5:c.2741delinsCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001079803.3:c.2741delinsCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001079804.3:c.2741delinsCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406741.1:c.2741delinsCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406742.1:c.2741delinsCAG - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004482631Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 7, 2023) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV005058750Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 4, 2024) 		unknownclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Characterization of immune response in Cross-Reactive Immunological Material (CRIM)-positive infantile Pompe disease patients treated with enzyme replacement therapy.

Desai AK, Kazi ZB, Bali DS, Kishnani PS.

Mol Genet Metab Rep. 2019 Sep;20:100475. doi: 10.1016/j.ymgmr.2019.100475.

PubMed [citation]
PMID:
31193175
PMCID:
PMC6518314

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 (8)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004482631.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This premature translational stop signal has been observed in individual(s) with Pompe disease (PMID: 22252923, 31193175). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the GAA protein in which other variant(s) (p.Tyr928Cys) have been determined to be pathogenic (PMID: 22252923, 29122469, 31606152, 33301762, 33741225). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change creates a premature translational stop signal (p.Gln914Profs*30) in the GAA gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 39 amino acid(s) of the GAA protein.

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

From Baylor Genetics, SCV005058750.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024