NM_000642.3(AGL):c.837C>A (p.His279Gln) AND Glycogen storage disease type III

Germline classification:: Uncertain significance (4 submissions)
Last evaluated:: Jul 15, 2021
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:: RCV000704543.12

Allele description [Variation Report for NM_000642.3(AGL):c.837C>A (p.His279Gln)]

NM_000642.3(AGL):c.837C>A (p.His279Gln)

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.837C>A (p.His279Gln)

HGVS:

NC_000001.11:g.99870572C>A
NG_012865.1:g.25489C>A
NM_000028.3:c.837C>A
NM_000642.3:c.837C>AMANE SELECT
NM_000643.3:c.837C>A
NM_000644.3:c.837C>A
NM_000646.3:c.789C>A
NM_001425325.1:c.837C>A
NM_001425326.1:c.837C>A
NM_001425327.1:c.837C>A
NM_001425328.1:c.633C>A
NM_001425329.1:c.633C>A
NM_001425332.1:c.459C>A
NP_000019.2:p.His279Gln
NP_000019.2:p.His279Gln
NP_000633.2:p.His279Gln
NP_000634.2:p.His279Gln
NP_000634.2:p.His279Gln
NP_000635.2:p.His279Gln
NP_000635.2:p.His279Gln
NP_000637.2:p.His263Gln
NP_000637.2:p.His263Gln
NP_001412254.1:p.His279Gln
NP_001412255.1:p.His279Gln
NP_001412256.1:p.His279Gln
NP_001412257.1:p.His211Gln
NP_001412258.1:p.His211Gln
NP_001412261.1:p.His153Gln
NC_000001.10:g.100336128C>A
NM_000028.2:c.837C>A
NM_000642.2:c.837C>A
NM_000643.2:c.837C>A
NM_000644.2:c.837C>A
NM_000646.2:c.789C>A

Protein change:

H153Q

Links:

dbSNP: rs1242665410

NCBI 1000 Genomes Browser:

rs1242665410

Molecular consequence:

NM_000028.3:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.789C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.837C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.633C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.633C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.459C>A - 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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Cambridgea pallidula voucher NZAC:03014771 histone 3 (H3) gene, partial cds
Cambridgea pallidula voucher NZAC:03014771 histone 3 (H3) gene, partial cds
gi|1735127278|gb|MK911556.1|

Nucleotide
Peripatoides sp. NZAC03005937 voucher NZAC:03005937 28S ribosomal RNA gene, part...
Peripatoides sp. NZAC03005937 voucher NZAC:03005937 28S ribosomal RNA gene, partial sequence
gi|285029465|gb|GQ911169.1|

Nucleotide
BioAssay by Target (List) for Gene (Select 20289) (3)
PubChem BioAssay
RefSeq RNA Links for Gene (Select 20289) (2)
Nucleotide
recombination-activating protein 1, partial [Spilocuscus maculatus]
recombination-activating protein 1, partial [Spilocuscus maculatus]
gi|223673671|gb|ACN12896.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000833495	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 7, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000896093	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 31, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001457967	Natera, Inc.	no assertion criteria provided	Uncertain significance (Jan 12, 2020)	germline	clinical testing
SCV002055086	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 15, 2021)	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	unknown	unknown	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

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

PMC

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.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000833495.4

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

Description

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. 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 glutamine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with AGL-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces histidine with glutamine at codon 279 of the AGL protein (p.His279Gln). The histidine residue is moderately conserved and there is a small physicochemical difference between histidine and glutamine.

#	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, SCV000896093.1

#	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 Natera, Inc., SCV001457967.1

#	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 Genome-Nilou Lab, SCV002055086.1

#	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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