NM_000642.3(AGL):c.1230_1233del (p.Gly411fs) AND Glycogen storage disease type III

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 27, 2017
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:: RCV000631141.2

Allele description [Variation Report for NM_000642.3(AGL):c.1230_1233del (p.Gly411fs)]

NM_000642.3(AGL):c.1230_1233del (p.Gly411fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.1230_1233del (p.Gly411fs)

HGVS:

NC_000001.11:g.99875398TGGC[1]
NG_012865.1:g.30315TGGC[1]
NM_000028.3:c.1226_1229TGGC[1]
NM_000642.3:c.1230_1233delMANE SELECT
NM_000643.3:c.1226_1229TGGC[1]
NM_000644.3:c.1226_1229TGGC[1]
NM_000646.3:c.1178_1181TGGC[1]
NM_001425325.1:c.1226_1229TGGC[1]
NM_001425326.1:c.1226_1229TGGC[1]
NM_001425328.1:c.1022_1025TGGC[1]
NM_001425329.1:c.1022_1025TGGC[1]
NM_001425332.1:c.848_851TGGC[1]
NP_000019.2:p.Gly411Metfs
NP_000019.2:p.Gly411fs
NP_000633.2:p.Gly411fs
NP_000634.2:p.Gly411Metfs
NP_000634.2:p.Gly411fs
NP_000635.2:p.Gly411Metfs
NP_000635.2:p.Gly411fs
NP_000637.2:p.Gly395Metfs
NP_000637.2:p.Gly395fs
NP_001412254.1:p.Gly411Metfs
NP_001412255.1:p.Gly411Metfs
NP_001412257.1:p.Gly343Metfs
NP_001412258.1:p.Gly343Metfs
NP_001412261.1:p.Gly285Metfs
NC_000001.10:g.100340954TGGC[1]
NM_000028.2:c.1230_1233del
NM_000642.2:c.1230_1233delTGGC
NM_000643.2:c.1230_1233del
NM_000644.2:c.1230_1233del
NM_000646.2:c.1182_1185del

Protein change:

G395fs

Links:

dbSNP: rs1553185474

NCBI 1000 Genomes Browser:

rs1553185474

Molecular consequence:

NM_000028.3:c.1226_1229TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000642.3:c.1230_1233del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000643.3:c.1226_1229TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000644.3:c.1226_1229TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000646.3:c.1178_1181TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425325.1:c.1226_1229TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425326.1:c.1226_1229TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425328.1:c.1022_1025TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425329.1:c.1022_1025TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425332.1:c.848_851TGGC[1] - frameshift variant - [Sequence Ontology: SO:0001589]

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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Olfactory receptor, family 8, subfamily B, member 12 [Homo sapiens]
Olfactory receptor, family 8, subfamily B, member 12 [Homo sapiens]
gi|187957510|gb|AAI36865.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000752139	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 27, 2017)	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

SCV000752139

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 27, 2017)

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, SCV000752139.1

#	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 creates a premature translational stop signal (p.Gly411Metfs*5) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with AGL-related disease. Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.

#	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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