NM_000152.5(GAA):c.1610del (p.Glu537fs) AND Glycogen storage disease, type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 6, 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:: RCV001937792.6

Allele description [Variation Report for NM_000152.5(GAA):c.1610del (p.Glu537fs)]

NM_000152.5(GAA):c.1610del (p.Glu537fs)

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_000152.5(GAA):c.1610del (p.Glu537fs)

HGVS:

NC_000017.11:g.80110999del
NG_009822.1:g.14444del
NM_000152.5:c.1610delMANE SELECT
NM_001079803.3:c.1610del
NM_001079804.3:c.1610del
NP_000143.2:p.Glu537fs
NP_001073271.1:p.Glu537fs
NP_001073272.1:p.Glu537fs
LRG_673:g.14444del
NC_000017.10:g.78084798del

Protein change:

E537fs

Links:

dbSNP: rs762060817

NCBI 1000 Genomes Browser:

rs762060817

Molecular consequence:

NM_000152.5:c.1610del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079803.3:c.1610del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079804.3:c.1610del - 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

Recent activity

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Microbulbifer okhotskensis strain OS29 NODE_627_length_204_cov_52.469799, whole ...
Microbulbifer okhotskensis strain OS29 NODE_627_length_204_cov_52.469799, whole genome shotgun sequence
gi|2260093532|ref|NZ_JALBWM01000062 gnl|WGS:NZ_JALBWM01|NODE_627_length_204_cov_52.469799

Nucleotide
Microbulbifer okhotskensis strain OS29 NODE_632_length_200_cov_51.400000, whole ...
Microbulbifer okhotskensis strain OS29 NODE_632_length_200_cov_51.400000, whole genome shotgun sequence
gi|2260093537|ref|NZ_JALBWM01000062 gnl|WGS:NZ_JALBWM01|NODE_632_length_200_cov_51.400000

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002184993	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 6, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 33560568, 18425781, 22252923, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002184993

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 6, 2023)

germline

clinical testing

PubMed (4)
[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

Update of the Pompe variant database for the prediction of clinical phenotypes: Novel disease-associated variants, common sequence variants, and results from newborn screening.

de Faria DOS, 't Groen SLMI, Hoogeveen-Westerveld M, Nino MY, van der Ploeg AT, Bergsma AJ, Pijnappel WWMP.

Hum Mutat. 2021 Feb;42(2):119-134. doi: 10.1002/humu.24148. Epub 2020 Dec 21.

PubMed [citation]

PMID:: 33560568
PMCID:: PMC7898817

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

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002184993.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1407438). This premature translational stop signal has been observed in individual(s) with Pompe disease (PMID: 33560568; Invitae). This variant is present in population databases (rs762060817, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Glu537Glyfs*41) 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).

#	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: Sep 29, 2024

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