NM_002103.5(GYS1):c.2207del (p.Arg736fs) AND Glycogen storage disease due to muscle and heart glycogen synthase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 8, 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:: RCV001068266.7

Allele description [Variation Report for NM_002103.5(GYS1):c.2207del (p.Arg736fs)]

NM_002103.5(GYS1):c.2207del (p.Arg736fs)

Gene:

GYS1:glycogen synthase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_002103.5(GYS1):c.2207del (p.Arg736fs)

HGVS:

NC_000019.10:g.48969295del
NG_012923.1:g.29059del
NM_001161587.2:c.2015del
NM_002103.5:c.2207delMANE SELECT
NP_001155059.1:p.Arg672fs
NP_002094.2:p.Arg736fs
NC_000019.9:g.49472552del
NM_002103.4:c.2207del
NR_027763.2:n.2222del

Protein change:

R672fs

Links:

dbSNP: rs2038513000

NCBI 1000 Genomes Browser:

rs2038513000

Molecular consequence:

NM_001161587.2:c.2015del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002103.5:c.2207del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_027763.2:n.2222del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Glycogen storage disease due to muscle and heart glycogen synthase deficiency
Synonyms:: GSD 0b; MUSCLE GLYCOGEN SYNTHASE DEFICIENCY
Identifiers:: MONDO: MONDO:0012693; MedGen: C1969054; Orphanet: 137625; OMIM: 611556

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001233365	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 8, 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

SCV001233365

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 8, 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, SCV001233365.6

#	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 results in a frameshift in the GYS1 gene (p.Arg736Leufs*106). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 2 amino acid(s) of the GYS1 protein and extend the protein by 103 additional amino acid residues. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GYS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 861694). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Feb 25, 2025

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