NM_000642.3(AGL):c.2522C>T (p.Ser841Phe) AND Glycogen storage disease type III

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Jan 31, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV001083232.19

Allele description [Variation Report for NM_000642.3(AGL):c.2522C>T (p.Ser841Phe)]

NM_000642.3(AGL):c.2522C>T (p.Ser841Phe)

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.2522C>T (p.Ser841Phe)

HGVS:

NC_000001.11:g.99884427C>T
NG_012865.1:g.39344C>T
NM_000028.3:c.2522C>T
NM_000642.3:c.2522C>TMANE SELECT
NM_000643.3:c.2522C>T
NM_000644.3:c.2522C>T
NM_000646.3:c.2474C>T
NM_001425325.1:c.2522C>T
NM_001425326.1:c.2522C>T
NM_001425327.1:c.2321C>T
NM_001425328.1:c.2318C>T
NM_001425329.1:c.2318C>T
NM_001425332.1:c.2144C>T
NP_000019.2:p.Ser841Phe
NP_000019.2:p.Ser841Phe
NP_000633.2:p.Ser841Phe
NP_000634.2:p.Ser841Phe
NP_000634.2:p.Ser841Phe
NP_000635.2:p.Ser841Phe
NP_000635.2:p.Ser841Phe
NP_000637.2:p.Ser825Phe
NP_000637.2:p.Ser825Phe
NP_001412254.1:p.Ser841Phe
NP_001412255.1:p.Ser841Phe
NP_001412256.1:p.Ser774Phe
NP_001412257.1:p.Ser773Phe
NP_001412258.1:p.Ser773Phe
NP_001412261.1:p.Ser715Phe
NC_000001.10:g.100349983C>T
NM_000028.2:c.2522C>T
NM_000642.2:c.2522C>T
NM_000643.2:c.2522C>T
NM_000644.2:c.2522C>T
NM_000646.2:c.2474C>T

Protein change:

S715F

Links:

dbSNP: rs150441555

NCBI 1000 Genomes Browser:

rs150441555

Molecular consequence:

NM_000028.3:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_000642.3:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_000643.3:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_000644.3:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_000646.3:c.2474C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425325.1:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425326.1:c.2522C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425327.1:c.2321C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425328.1:c.2318C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425329.1:c.2318C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425332.1:c.2144C>T - 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

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
SCV000626698	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001258890	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV001457982	Natera, Inc.	no assertion criteria provided	Benign (Jan 6, 2020)	germline	clinical testing
SCV002055538	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000626698.9

#	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 Illumina Laboratory Services, Illumina, SCV001258890.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown 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., SCV001457982.1

#	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, SCV002055538.1

#	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: Oct 20, 2024

ClinVar

Relating variation to medicine