NM_000152.5(GAA):c.1950_1952delinsT (p.Gly651fs) AND Glycogen storage disease, type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 1, 2020
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:: RCV003867382.2

Allele description [Variation Report for NM_000152.5(GAA):c.1950_1952delinsT (p.Gly651fs)]

NM_000152.5(GAA):c.1950_1952delinsT (p.Gly651fs)

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_000152.5(GAA):c.1950_1952delinsT (p.Gly651fs)

HGVS:

NC_000017.11:g.80112937_80112939delinsT
NG_009822.1:g.16382_16384delinsT
NG_137936.1:g.222_224delinsT
NM_000152.5:c.1950_1952delinsTMANE SELECT
NM_001079803.3:c.1950_1952delinsT
NM_001079804.3:c.1950_1952delinsT
NM_001406741.1:c.1950_1952delinsT
NM_001406742.1:c.1950_1952delinsT
NP_000143.2:p.Gly651Glnfs
NP_000143.2:p.Gly651fs
NP_001073271.1:p.Gly651fs
NP_001073272.1:p.Gly651fs
NP_001393670.1:p.Gly651fs
NP_001393671.1:p.Gly651fs
LRG_673t1:c.1950_1952delGGGinsT
LRG_673:g.16382_16384delinsT
LRG_673p1:p.Gly651Glnfs
NC_000017.10:g.78086736_78086738delinsT
NM_000152.3:c.1950_1952delGGGinsT

Protein change:

G651fs

Molecular consequence:

NM_000152.5:c.1950_1952delinsT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079803.3:c.1950_1952delinsT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079804.3:c.1950_1952delinsT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406741.1:c.1950_1952delinsT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406742.1:c.1950_1952delinsT - 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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biosample
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PREDICTED: Homo sapiens nucleic acid binding protein 1 (NABP1), transcript variant X2, mRNA
gi|2462576133|ref|XM_054343423.1|

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Nucleotide
qn04c12.x1 NCI_CGAP_Lu5 Homo sapiens cDNA clone IMAGE:1897270 3', mRNA sequence
qn04c12.x1 NCI_CGAP_Lu5 Homo sapiens cDNA clone IMAGE:1897270 3', mRNA sequence
gi|3960534|gnl|dbEST|2074985|gb|AI3 .1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004672489	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 1, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18425781, 22252923, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004672489

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 1, 2020)

germline

clinical testing

PubMed (3)
[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 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

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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004672489.1

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in GAA are known to be pathogenic (PMID: 18425781, 22252923). This variant has not been reported in the literature in individuals with GAA-related conditions. ClinVar contains an entry for this variant (Variation ID: 632822). The frequency data for this variant in the population databases is not available, as this variant may be reported as separate entries in the ExAC database. This sequence change creates a premature translational stop signal (p.Gly651Glnfs*85) in the GAA gene. It is expected to result in an absent or disrupted protein product.

#	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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