NM_021957.4(GYS2):c.710_711delinsCC (p.Gln237Pro) AND Glycogen storage disorder due to hepatic glycogen synthase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 2, 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:: RCV002579404.3

Allele description [Variation Report for NM_021957.4(GYS2):c.710_711delinsCC (p.Gln237Pro)]

NM_021957.4(GYS2):c.710_711delinsCC (p.Gln237Pro)

Gene:

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

Variant type:

Indel

Cytogenetic location:

12p12.1

Genomic location:

Preferred name:

NM_021957.4(GYS2):c.710_711delinsCC (p.Gln237Pro)

HGVS:

NC_000012.12:g.21568977_21568978delinsGG
NG_016167.1:g.40870_40871delinsCC
NM_021957.4:c.710_711delinsCCMANE SELECT
NP_068776.2:p.Gln237Pro
LRG_1293t1:c.710_711delinsCC
LRG_1293:g.40870_40871delinsCC
LRG_1293p1:p.Gln237Pro
NC_000012.11:g.21721911_21721912delinsGG

Protein change:

Q237P

Molecular consequence:

NM_021957.4:c.710_711delinsCC - missense variant - [Sequence Ontology: SO:0001583]

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
SCV003489700	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 2, 2024)	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

SCV003489700

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 2, 2024)

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, SCV003489700.2

#	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 glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 237 of the GYS2 protein (p.Gln237Pro). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with GYS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2175667). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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

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