NM_000152.5(GAA):c.138C>T (p.Ser46=) AND Glycogen storage disease, type II

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 2, 2024
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:: RCV000977371.10

Allele description [Variation Report for NM_000152.5(GAA):c.138C>T (p.Ser46=)]

NM_000152.5(GAA):c.138C>T (p.Ser46=)

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.138C>T (p.Ser46=)

HGVS:

NC_000017.11:g.80104724C>T
NG_009822.1:g.8169C>T
NM_000152.5:c.138C>TMANE SELECT
NM_001079803.3:c.138C>T
NM_001079804.3:c.138C>T
NP_000143.2:p.Ser46=
NP_001073271.1:p.Ser46=
NP_001073272.1:p.Ser46=
LRG_673t1:c.138C>T
LRG_673:g.8169C>T
NC_000017.10:g.78078523C>T
NM_000152.3:c.138C>T

Links:

dbSNP: rs753375900

NCBI 1000 Genomes Browser:

rs753375900

Molecular consequence:

NM_000152.5:c.138C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001079803.3:c.138C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001079804.3:c.138C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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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LOC125680841 [Ostrea edulis]
LOC125680841 [Ostrea edulis]
Gene ID:125680841

Gene
LOC125680402 [Ostrea edulis]
LOC125680402 [Ostrea edulis]
Gene ID:125680402

Gene
Histiocytosis
Histiocytosis
General term for the abnormal appearance of histiocytes in the blood. Based on the pathological features of the cells involved rather than on clinical findings, the histiocyti...<br/>Year introduced: 1990

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001125287	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 2, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001463466	Natera, Inc.	no assertion criteria provided	Uncertain significance (Mar 10, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001125287

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 2, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001463466

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Mar 10, 2020)

germline

clinical testing

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001125287.6

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

#	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

From Natera, Inc., SCV001463466.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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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