NM_000642.3(AGL):c.1395T>G (p.Asp465Glu) AND Glycogen storage disease type III

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 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:: RCV002615388.1

Allele description

NM_000642.3(AGL):c.1395T>G (p.Asp465Glu)

Gene:

AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.1395T>G (p.Asp465Glu)

HGVS:

NC_000001.11:g.99876569T>G
NG_012865.1:g.31486T>G
NM_000028.3:c.1395T>G
NM_000642.3:c.1395T>GMANE SELECT
NM_000643.3:c.1395T>G
NM_000644.3:c.1395T>G
NM_000646.3:c.1347T>G
NM_001425325.1:c.1395T>G
NM_001425326.1:c.1395T>G
NM_001425327.1:c.1194T>G
NM_001425328.1:c.1191T>G
NM_001425329.1:c.1191T>G
NM_001425332.1:c.1017T>G
NP_000019.2:p.Asp465Glu
NP_000019.2:p.Asp465Glu
NP_000633.2:p.Asp465Glu
NP_000634.2:p.Asp465Glu
NP_000634.2:p.Asp465Glu
NP_000635.2:p.Asp465Glu
NP_000635.2:p.Asp465Glu
NP_000637.2:p.Asp449Glu
NP_000637.2:p.Asp449Glu
NP_001412254.1:p.Asp465Glu
NP_001412255.1:p.Asp465Glu
NP_001412256.1:p.Asp398Glu
NP_001412257.1:p.Asp397Glu
NP_001412258.1:p.Asp397Glu
NP_001412261.1:p.Asp339Glu
NC_000001.10:g.100342125T>G
NM_000028.2:c.1395T>G
NM_000643.2:c.1395T>G
NM_000644.2:c.1395T>G
NM_000646.2:c.1347T>G

Protein change:

D339E

Molecular consequence:

NM_000028.3:c.1395T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.1395T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.1395T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.1395T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.1347T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.1395T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.1395T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.1194T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.1191T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.1191T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.1017T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glycogen storage disease type III (GSD3)
Synonyms:: Glycogen storage disease type 3; Forbes disease; Cori disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009291; MedGen: C0017922; Orphanet: 366; OMIM: 232400

Recent activity

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proto-oncogene tyrosine-protein kinase Src isoform 2 [Mus musculus]
proto-oncogene tyrosine-protein kinase Src isoform 2 [Mus musculus]
gi|2316837799|ref|NP_001399620.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003500322	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 6, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003500322

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 6, 2022)

germline

clinical testing

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

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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 Invitae, SCV003500322.1

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 465 of the AGL protein (p.Asp465Glu). This variant is present in population databases (rs768623422, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with AGL-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Nov 20, 2023

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