NM_000642.3(AGL):c.1139A>G (p.Glu380Gly) AND Glycogen storage disease type III

Germline classification:: Uncertain significance (4 submissions)
Last evaluated:: Apr 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001326081.10

Allele description [Variation Report for NM_000642.3(AGL):c.1139A>G (p.Glu380Gly)]

NM_000642.3(AGL):c.1139A>G (p.Glu380Gly)

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.1139A>G (p.Glu380Gly)

HGVS:

NC_000001.11:g.99875210A>G
NG_012865.1:g.30127A>G
NM_000028.3:c.1139A>G
NM_000642.3:c.1139A>GMANE SELECT
NM_000643.3:c.1139A>G
NM_000644.3:c.1139A>G
NM_000646.3:c.1091A>G
NM_001425325.1:c.1139A>G
NM_001425326.1:c.1139A>G
NM_001425328.1:c.935A>G
NM_001425329.1:c.935A>G
NM_001425332.1:c.761A>G
NP_000019.2:p.Glu380Gly
NP_000019.2:p.Glu380Gly
NP_000633.2:p.Glu380Gly
NP_000634.2:p.Glu380Gly
NP_000634.2:p.Glu380Gly
NP_000635.2:p.Glu380Gly
NP_000635.2:p.Glu380Gly
NP_000637.2:p.Glu364Gly
NP_000637.2:p.Glu364Gly
NP_001412254.1:p.Glu380Gly
NP_001412255.1:p.Glu380Gly
NP_001412257.1:p.Glu312Gly
NP_001412258.1:p.Glu312Gly
NP_001412261.1:p.Glu254Gly
NC_000001.10:g.100340766A>G
NM_000028.2:c.1139A>G
NM_000643.2:c.1139A>G
NM_000644.2:c.1139A>G
NM_000646.2:c.1091A>G

Protein change:

E254G

Links:

dbSNP: rs1045745115

NCBI 1000 Genomes Browser:

rs1045745115

Molecular consequence:

NM_000028.3:c.1139A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.1139A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.1139A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.1139A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.1091A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.1139A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.1139A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.935A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.935A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.761A>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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Homo sapiens paired-like homeodomain 2 (PITX2), transcript variant 1, mRNA
Homo sapiens paired-like homeodomain 2 (PITX2), transcript variant 1, mRNA
gi|24234710|ref|NM_153427.1|

Nucleotide
Homo sapiens paired-like homeodomain 2 (PITX2), transcript variant 2, mRNA
Homo sapiens paired-like homeodomain 2 (PITX2), transcript variant 2, mRNA
gi|24234707|ref|NM_153426.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001517095	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 28, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002091475	Natera, Inc.	no assertion criteria provided	Uncertain significance (Jul 14, 2021)	germline	clinical testing
SCV002814235	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 5, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004049950	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 11, 2023)	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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001517095.3

#	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 glutamic acid with glycine at codon 380 of the AGL protein (p.Glu380Gly). The glutamic acid residue is moderately conserved and there is a moderate physicochemical difference between glutamic acid and glycine. This variant is not present in population databases (ExAC 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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

From Natera, Inc., SCV002091475.1

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002814235.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004049950.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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