NM_000642.3(AGL):c.4465_4467del (p.Tyr1489del) AND Glycogen storage disease type III

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 11, 2023
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:: RCV000672173.5

Allele description [Variation Report for NM_000642.3(AGL):c.4465_4467del (p.Tyr1489del)]

NM_000642.3(AGL):c.4465_4467del (p.Tyr1489del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.4465_4467del (p.Tyr1489del)

HGVS:

NC_000001.11:g.99916715_99916717del
NG_012865.1:g.71632_71634del
NM_000028.3:c.4465_4467delTAT
NM_000642.3:c.4465_4467delMANE SELECT
NM_000643.3:c.4465_4467delTAT
NM_000644.3:c.4465_4467delTAT
NM_000646.3:c.4417_4419delTAT
NM_001425325.1:c.4465_4467delTAT
NM_001425326.1:c.4444_4446delTAT
NM_001425327.1:c.4264_4266delTAT
NM_001425328.1:c.4261_4263delTAT
NM_001425329.1:c.4126_4128delTAT
NM_001425332.1:c.4087_4089delTAT
NP_000019.2:p.Tyr1489del
NP_000019.2:p.Tyr1489del
NP_000633.2:p.Tyr1489del
NP_000634.2:p.Tyr1489del
NP_000634.2:p.Tyr1489del
NP_000635.2:p.Tyr1489del
NP_000635.2:p.Tyr1489del
NP_000637.2:p.Tyr1473del
NP_000637.2:p.Tyr1473del
NP_001412254.1:p.Tyr1489del
NP_001412255.1:p.Tyr1482del
NP_001412256.1:p.Tyr1422del
NP_001412257.1:p.Tyr1421del
NP_001412258.1:p.Tyr1376del
NP_001412261.1:p.Tyr1363del
NC_000001.10:g.100382269_100382271del
NC_000001.10:g.100382271_100382273del
NM_000028.2:c.4465_4467del
NM_000642.2:c.4465_4467delTAT
NM_000643.2:c.4465_4467del
NM_000644.2:c.4465_4467del
NM_000646.2:c.4417_4419del

Protein change:

Y1363del

Links:

dbSNP: rs1553193523

NCBI 1000 Genomes Browser:

rs1553193523

Molecular consequence:

NM_000642.3:c.4465_4467del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_000028.3:c.4465_4467delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_000643.3:c.4465_4467delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_000644.3:c.4465_4467delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_000646.3:c.4417_4419delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001425325.1:c.4465_4467delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001425326.1:c.4444_4446delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001425327.1:c.4264_4266delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001425328.1:c.4261_4263delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001425329.1:c.4126_4128delTAT - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001425332.1:c.4087_4089delTAT - inframe_indel - [Sequence Ontology: SO:0001820]

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
SCV000797252	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Jan 18, 2018)	unknown	clinical testing	Citation Link,
SCV003348657	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 2, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004050099	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 11, 2023)	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

SCV000797252

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Jan 18, 2018)

unknown

clinical testing

Citation Link,

SCV003348657

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 2, 2022)

germline

clinical testing

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

SCV004050099

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 11, 2023)

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	germline	unknown	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

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 Counsyl, SCV000797252.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003348657.2

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

Description

This variant, c.4465_4467del, results in the deletion of 1 amino acid(s) of the AGL protein (p.Tyr1489del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 556204). This variant has not been reported in the literature in individuals affected with AGL-related conditions.

#	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, SCV004050099.1

#	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

ClinVar

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