NC_000017.11:g.(?_80107537)_(80113386_?)del AND Glycogen storage disease, type II

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 11, 2017
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:: RCV000631119.1

Allele description [Variation Report for NC_000017.11:g.(?_80107537)_(80113386_?)del]

NC_000017.11:g.(?_80107537)_(80113386_?)del

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NC_000017.11:g.(?_80107537)_(80113386_?)del

HGVS:

NC_000017.11:g.(?_80107537)_(80113386_?)del
NC_000017.10:g.(?_78081336)_(78087185_?)del

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000752114	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Dec 11, 2017)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 18429042, 17723315, 10338092, 21039225, 11738358, 9535769, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000752114

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Dec 11, 2017)

germline

clinical testing

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

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

Molecular and functional characterization of eight novel GAA mutations in Italian infants with Pompe disease.

Pittis MG, Donnarumma M, Montalvo AL, Dominissini S, Kroos M, Rosano C, Stroppiano M, Bianco MG, Donati MA, Parenti G, D'Amico A, Ciana G, Di Rocco M, Reuser A, Bembi B, Filocamo M.

Hum Mutat. 2008 Jun;29(6):E27-36. doi: 10.1002/humu.20753.

PubMed [citation]

PMID:: 18429042

Development of a clinical assay for detection of GAA mutations and characterization of the GAA mutation spectrum in a Canadian cohort of individuals with glycogen storage disease, type II.

McCready ME, Carson NL, Chakraborty P, Clarke JT, Callahan JW, Skomorowski MA, Chan AK, Bamforth F, Casey R, Rupar CA, Geraghty MT.

Mol Genet Metab. 2007 Dec;92(4):325-35. Epub 2007 Aug 27.

PubMed [citation]

PMID:: 17723315

See all PubMed Citations (7)

Details of each submission

From Invitae, SCV000752114.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This variant is an in-frame deletion of the genomic region encompassing exons 4-15 of the GAA gene. It preserves the integrity of the reading frame. This variant has not been reported in the literature in individuals with GAA-related disease. Several sequence variants in exons 4-15 have been determined to be pathogenic (PMID: 11738358, 18429042, 9535769, 17723315, 10338092, 21039225, 17723315). This suggests that these exons are critical for GAA protein function and that loss of these exons may also be pathogenic. 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.

#	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: Mar 18, 2023

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