NM_000642.3(AGL):c.1895T>C (p.Ile632Thr) AND Glycogen storage disease type III

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 29, 2024
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:: RCV000559891.12

Allele description [Variation Report for NM_000642.3(AGL):c.1895T>C (p.Ile632Thr)]

NM_000642.3(AGL):c.1895T>C (p.Ile632Thr)

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.1895T>C (p.Ile632Thr)

HGVS:

NC_000001.11:g.99880791T>C
NG_012865.1:g.35708T>C
NM_000028.3:c.1895T>C
NM_000642.3:c.1895T>CMANE SELECT
NM_000643.3:c.1895T>C
NM_000644.3:c.1895T>C
NM_000646.3:c.1847T>C
NM_001425325.1:c.1895T>C
NM_001425326.1:c.1895T>C
NM_001425327.1:c.1694T>C
NM_001425328.1:c.1691T>C
NM_001425329.1:c.1691T>C
NM_001425332.1:c.1517T>C
NP_000019.2:p.Ile632Thr
NP_000019.2:p.Ile632Thr
NP_000633.2:p.Ile632Thr
NP_000634.2:p.Ile632Thr
NP_000634.2:p.Ile632Thr
NP_000635.2:p.Ile632Thr
NP_000635.2:p.Ile632Thr
NP_000637.2:p.Ile616Thr
NP_000637.2:p.Ile616Thr
NP_001412254.1:p.Ile632Thr
NP_001412255.1:p.Ile632Thr
NP_001412256.1:p.Ile565Thr
NP_001412257.1:p.Ile564Thr
NP_001412258.1:p.Ile564Thr
NP_001412261.1:p.Ile506Thr
NC_000001.10:g.100346347T>C
NM_000028.2:c.1895T>C
NM_000642.2:c.1895T>C
NM_000643.2:c.1895T>C
NM_000644.2:c.1895T>C
NM_000646.2:c.1847T>C

Protein change:

I506T

Links:

dbSNP: rs138823746

NCBI 1000 Genomes Browser:

rs138823746

Molecular consequence:

NM_000028.3:c.1895T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.1895T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.1895T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.1895T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.1847T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.1895T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.1895T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.1694T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.1691T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.1691T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.1517T>C - 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
SCV000626682	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002091518	Natera, Inc.	no assertion criteria provided	Uncertain significance (Oct 28, 2019)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000626682

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 29, 2024)

germline

clinical testing

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

SCV002091518

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Oct 28, 2019)

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, SCV000626682.9

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

From Natera, Inc., SCV002091518.1

#	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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