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NM_000152.5(GAA):c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC AND Glycogen storage disease, type II

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 6, 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:
RCV002780301.3

Allele description [Variation Report for NM_000152.5(GAA):c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC]

NM_000152.5(GAA):c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC

Gene:
GAA:alpha glucosidase [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_000152.5(GAA):c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
HGVS:
  • NC_000017.11:g.80104538_80104545delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
  • NG_009822.1:g.7983_7990delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
  • NM_000152.5:c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGCMANE SELECT
  • NM_001079803.3:c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
  • NM_001079804.3:c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
  • LRG_673:g.7983_7990delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
  • NC_000017.10:g.78078337_78078344delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC
Molecular consequence:
  • NM_000152.5:c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001079803.3:c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001079804.3:c.-32-17_-32-10delinsTCCCTGCTGAGCCTCCTACAGGCCTCCCGC - intron variant - [Sequence Ontology: SO:0001627]

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
SCV003023242Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Oct 6, 2022) 		germlineclinical testing

PubMed (9)
[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

[The physiology of bed rest].

Rubin M.

Servir. 1989 Jul-Aug;37(4):234-9. Portuguese. No abstract available.

PubMed [citation]
PMID:
2510307

Aberrant splicing in adult onset glycogen storage disease type II (GSDII): molecular identification of an IVS1 (-13T-->G) mutation in a majority of patients and a novel IVS10 (+1GT-->CT) mutation.

Huie ML, Chen AS, Tsujino S, Shanske S, DiMauro S, Engel AG, Hirschhorn R.

Hum Mol Genet. 1994 Dec;3(12):2231-6.

PubMed [citation]
PMID:
7881425
See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003023242.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the c.-32-13T nucleotide in the GAA gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 2510307, 7881425, 21439876, 22613277, 24245577, 24590251, 26231297). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has been observed in individual(s) with Pompe disease (PMID: 25037089). This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 1 of the GAA gene. It does not directly change the encoded amino acid sequence of the GAA protein.

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

Last Updated: Sep 29, 2024