NM_000642.3(AGL):c.795A>C (p.Lys265Asn) AND Glycogen storage disease type III

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 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:: RCV001369236.6

Allele description [Variation Report for NM_000642.3(AGL):c.795A>C (p.Lys265Asn)]

NM_000642.3(AGL):c.795A>C (p.Lys265Asn)

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.795A>C (p.Lys265Asn)

HGVS:

NC_000001.11:g.99870530A>C
NG_012865.1:g.25447A>C
NM_000028.3:c.795A>C
NM_000642.3:c.795A>CMANE SELECT
NM_000643.3:c.795A>C
NM_000644.3:c.795A>C
NM_000646.3:c.747A>C
NM_001425325.1:c.795A>C
NM_001425326.1:c.795A>C
NM_001425327.1:c.795A>C
NM_001425328.1:c.591A>C
NM_001425329.1:c.591A>C
NM_001425332.1:c.417A>C
NP_000019.2:p.Lys265Asn
NP_000019.2:p.Lys265Asn
NP_000633.2:p.Lys265Asn
NP_000634.2:p.Lys265Asn
NP_000634.2:p.Lys265Asn
NP_000635.2:p.Lys265Asn
NP_000635.2:p.Lys265Asn
NP_000637.2:p.Lys249Asn
NP_000637.2:p.Lys249Asn
NP_001412254.1:p.Lys265Asn
NP_001412255.1:p.Lys265Asn
NP_001412256.1:p.Lys265Asn
NP_001412257.1:p.Lys197Asn
NP_001412258.1:p.Lys197Asn
NP_001412261.1:p.Lys139Asn
NC_000001.10:g.100336086A>C
NM_000028.2:c.795A>C
NM_000643.2:c.795A>C
NM_000644.2:c.795A>C
NM_000646.2:c.747A>C

Protein change:

K139N

Links:

dbSNP: rs1441216143

NCBI 1000 Genomes Browser:

rs1441216143

Molecular consequence:

NM_000028.3:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.747A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.795A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.591A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.591A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.417A>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

Recent activity

Clear Turn Off Turn On

LOC18431074 [Amborella trichopoda]
LOC18431074 [Amborella trichopoda]
Gene ID:18431074

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001565669	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	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

SCV001565669

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

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, SCV001565669.3

#	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 lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 265 of the AGL protein (p.Lys265Asn). This variant is present in population databases (no rsID available, gnomAD 0.0009%). 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: 1059876). 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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine