NM_000642.3(AGL):c.1311A>G (p.Ile437Met) AND Glycogen storage disease type III

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 15, 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:: RCV002800161.2

Allele description [Variation Report for NM_000642.3(AGL):c.1311A>G (p.Ile437Met)]

NM_000642.3(AGL):c.1311A>G (p.Ile437Met)

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.1311A>G (p.Ile437Met)

HGVS:

NC_000001.11:g.99876485A>G
NG_012865.1:g.31402A>G
NM_000028.3:c.1311A>G
NM_000642.3:c.1311A>GMANE SELECT
NM_000643.3:c.1311A>G
NM_000644.3:c.1311A>G
NM_000646.3:c.1263A>G
NM_001425325.1:c.1311A>G
NM_001425326.1:c.1311A>G
NM_001425327.1:c.1110A>G
NM_001425328.1:c.1107A>G
NM_001425329.1:c.1107A>G
NM_001425332.1:c.933A>G
NP_000019.2:p.Ile437Met
NP_000019.2:p.Ile437Met
NP_000633.2:p.Ile437Met
NP_000634.2:p.Ile437Met
NP_000634.2:p.Ile437Met
NP_000635.2:p.Ile437Met
NP_000635.2:p.Ile437Met
NP_000637.2:p.Ile421Met
NP_000637.2:p.Ile421Met
NP_001412254.1:p.Ile437Met
NP_001412255.1:p.Ile437Met
NP_001412256.1:p.Ile370Met
NP_001412257.1:p.Ile369Met
NP_001412258.1:p.Ile369Met
NP_001412261.1:p.Ile311Met
NC_000001.10:g.100342041A>G
NM_000028.2:c.1311A>G
NM_000643.2:c.1311A>G
NM_000644.2:c.1311A>G
NM_000646.2:c.1263A>G

Protein change:

I311M

Molecular consequence:

NM_000028.3:c.1311A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.1311A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.1311A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.1311A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.1263A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.1311A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.1311A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.1110A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.1107A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.1107A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.933A>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003022047	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 15, 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

SCV003022047

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 15, 2022)

germline

clinical testing

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

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, SCV003022047.1

#	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 isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 437 of the AGL protein (p.Ile437Met). This variant is not present in population databases (gnomAD no frequency). 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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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: Sep 29, 2024

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