NM_021957.4(GYS2):c.942-7del AND Glycogen storage disorder due to hepatic glycogen synthase deficiency

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 29, 2023
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:: RCV000300407.11

Allele description [Variation Report for NM_021957.4(GYS2):c.942-7del]

NM_021957.4(GYS2):c.942-7del

Gene:

GYS2:glycogen synthase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12p12.1

Genomic location:

Preferred name:

NM_021957.4(GYS2):c.942-7del

HGVS:

NC_000012.12:g.21563045del
NG_016167.1:g.46803del
NM_021957.4:c.942-7delMANE SELECT
LRG_1293t1:c.942-7del
LRG_1293:g.46803del
NC_000012.11:g.21715979del
NM_021957.3:c.942-7delG

Links:

dbSNP: rs537907545

NCBI 1000 Genomes Browser:

rs537907545

Molecular consequence:

NM_021957.4:c.942-7del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Glycogen storage disorder due to hepatic glycogen synthase deficiency
Synonyms:: GSD 0a; LIVER GLYCOGEN SYNTHASE DEFICIENCY; Hypoglycemia with deficiency of glycogen synthetase in the liver; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009414; MedGen: C1855861; Orphanet: 2089; OMIM: 240600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000377441	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Uncertain significance (Jun 14, 2016)	germline	clinical testing	ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV002344210	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Oct 29, 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

SCV000377441

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification 20161018)

Uncertain significance
(Jun 14, 2016)

germline

clinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV002344210

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Oct 29, 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	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 Illumina Laboratory Services, Illumina, SCV000377441.2

#	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 Invitae, SCV002344210.3

#	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

Last Updated: May 19, 2024

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