NC_000017.10:g.(78091549_78091991)_(78092157_78092451)del AND Glycogen storage disease, type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 15, 2023
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:: RCV003226643.1

Allele description [Variation Report for NC_000017.10:g.(78091549_78091991)_(78092157_78092451)del]

NC_000017.10:g.(78091549_78091991)_(78092157_78092451)del

Gene:: GAA:alpha glucosidase [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 17q25.3
Genomic location:: Chr17: 78091549 - 78092451 (on Assembly GRCh37)
Preferred name:: NC_000017.10:g.(78091549_78091991)_(78092157_78092451)del
HGVS:: NC_000017.10:g.(78091549_78091991)_(78092157_78092451)del
This HGVS expression did not pass validation

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
SCV003922539	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Mar 15, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 7945303, 32248831, 7981676 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003922539

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Mar 15, 2023)

germline

clinical testing

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

Citation Link

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

Deletion of exon 18 is a frequent mutation in glycogen storage disease type II.

Van der Kraan M, Kroos MA, Joosse M, Bijvoet AG, Verbeet MP, Kleijer WJ, Reuser AJ.

Biochem Biophys Res Commun. 1994 Sep 30;203(3):1535-41.

PubMed [citation]

PMID:: 7945303

Late-onset Pompe disease (LOPD) in Belgium: clinical characteristics and outcome measures.

Vanherpe P, Fieuws S, D'Hondt A, Bleyenheuft C, Demaerel P, De Bleecker J, Van den Bergh P, Baets J, Remiche G, Verhoeven K, Delstanche S, Toussaint M, Buyse B, Van Damme P, Depuydt CE, Claeys KG.

Orphanet J Rare Dis. 2020 Apr 5;15(1):83. doi: 10.1186/s13023-020-01353-4.

PubMed [citation]

PMID:: 32248831
PMCID:: PMC7133011

See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003922539.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

Variant summary: The variant identified by MLPA or other technology involves the deletion of exon 18 in the GAA gene. A presumed nomenclature of c.(2481+1_2482-1)_(2646+1_2647-1)del has been designated for the purposes of this classification. It is expected to result in a large in-frame deletion change in the GAA gene, a known mechanism of disease. An exon 18 deletion allele was found at a frequency of 4.6e-05 in 21694 control chromosomes (gnomAD, Structural Variants dataset). Deletion of exon 18 has been reported in the literature in multiple individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) (e.g. Huie_1994, Van der Kraan_1994, Vanherpe_2020). These data indicate that the variant is very likely to be associated with disease. Three submitters have provided clinical-significance assessments for exon 18 deletion variants to ClinVar after 2014 , and all laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as 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: May 13, 2023

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