NM_000642.3(AGL):c.3419T>G (p.Leu1140Arg) AND Glycogen storage disease type III

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 1, 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:: RCV001230541.7

Allele description [Variation Report for NM_000642.3(AGL):c.3419T>G (p.Leu1140Arg)]

NM_000642.3(AGL):c.3419T>G (p.Leu1140Arg)

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.3419T>G (p.Leu1140Arg)

HGVS:

NC_000001.11:g.99900692T>G
NG_012865.1:g.55609T>G
NM_000028.3:c.3419T>G
NM_000642.3:c.3419T>GMANE SELECT
NM_000643.3:c.3419T>G
NM_000644.3:c.3419T>G
NM_000646.3:c.3371T>G
NM_001425325.1:c.3419T>G
NM_001425326.1:c.3398T>G
NM_001425327.1:c.3218T>G
NM_001425328.1:c.3215T>G
NM_001425329.1:c.3080T>G
NM_001425332.1:c.3041T>G
NP_000019.2:p.Leu1140Arg
NP_000019.2:p.Leu1140Arg
NP_000633.2:p.Leu1140Arg
NP_000634.2:p.Leu1140Arg
NP_000634.2:p.Leu1140Arg
NP_000635.2:p.Leu1140Arg
NP_000635.2:p.Leu1140Arg
NP_000637.2:p.Leu1124Arg
NP_000637.2:p.Leu1124Arg
NP_001412254.1:p.Leu1140Arg
NP_001412255.1:p.Leu1133Arg
NP_001412256.1:p.Leu1073Arg
NP_001412257.1:p.Leu1072Arg
NP_001412258.1:p.Leu1027Arg
NP_001412261.1:p.Leu1014Arg
NC_000001.10:g.100366248T>G
NM_000028.2:c.3419T>G
NM_000642.2:c.3419T>G
NM_000643.2:c.3419T>G
NM_000644.2:c.3419T>G
NM_000646.2:c.3371T>G

Protein change:

L1014R

Links:

dbSNP: rs568139822

NCBI 1000 Genomes Browser:

rs568139822

Molecular consequence:

NM_000028.3:c.3419T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.3419T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.3419T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.3419T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.3371T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.3419T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.3398T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.3218T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.3215T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.3080T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.3041T>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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gi|1147537|gnl|dbEST|430676|gb|N293

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001403023	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002094532	Natera, Inc.	no assertion criteria provided	Uncertain significance (Mar 24, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001403023

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2022)

germline

clinical testing

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

SCV002094532

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Mar 24, 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, SCV001403023.4

#	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 leucine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 1140 of the AGL protein (p.Leu1140Arg). This variant is present in population databases (rs568139822, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with AGL-related conditions. ClinVar contains an entry for this variant (Variation ID: 957549). 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: "Deleterious"; PolyPhen-2: "Probably 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

From Natera, Inc., SCV002094532.1

#	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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