NM_000152.5(GAA):c.2619C>G (p.Tyr873Ter) AND Glycogen storage disease, type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 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:: RCV003112391.5

Allele description [Variation Report for NM_000152.5(GAA):c.2619C>G (p.Tyr873Ter)]

NM_000152.5(GAA):c.2619C>G (p.Tyr873Ter)

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_000152.5(GAA):c.2619C>G (p.Tyr873Ter)

HGVS:

NC_000017.11:g.80118330C>G
NG_009822.1:g.21775C>G
NM_000152.5:c.2619C>GMANE SELECT
NM_001079803.3:c.2619C>G
NM_001079804.3:c.2619C>G
NM_001406741.1:c.2619C>G
NM_001406742.1:c.2619C>G
NP_000143.2:p.Tyr873Ter
NP_000143.2:p.Tyr873Ter
NP_001073271.1:p.Tyr873Ter
NP_001073272.1:p.Tyr873Ter
NP_001393670.1:p.Tyr873Ter
NP_001393671.1:p.Tyr873Ter
LRG_673t1:c.2619C>G
LRG_673:g.21775C>G
LRG_673p1:p.Tyr873Ter
NC_000017.10:g.78092129C>G
NM_000152.3:c.2619C>G

Protein change:

Y873*

Molecular consequence:

NM_000152.5:c.2619C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001079803.3:c.2619C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001079804.3:c.2619C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001406741.1:c.2619C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001406742.1:c.2619C>G - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003787137	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 6, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23417379, 18425781, 22252923, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003787137

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 6, 2022)

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

Double trouble in a patient with myotonia.

Hehir MK, Logigian E, Raja Rayan DL, Ciafaloni E.

BMJ Case Rep. 2013 Feb 14;2013. doi:pii: bcr-2012-008167. 10.1136/bcr-2012-008167.

PubMed [citation]

PMID:: 23417379
PMCID:: PMC3604294

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, SCV003787137.3

#	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. This premature translational stop signal has been observed in individual(s) with GAA-related conditions (PMID: 23417379). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr873*) 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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