NM_002103.5(GYS1):c.1615G>T (p.Glu539Ter) AND Glycogen storage disease 0, muscle

Clinical significance:Pathogenic (Last evaluated: Sep 17, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000691851.1

Allele description [Variation Report for NM_002103.5(GYS1):c.1615G>T (p.Glu539Ter)]

NM_002103.5(GYS1):c.1615G>T (p.Glu539Ter)

Genes:
LOC119369037:CRISPRi-FlowFISH-validated FTL regulatory element [Gene]
GYS1:glycogen synthase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.33
Genomic location:
Preferred name:
NM_002103.5(GYS1):c.1615G>T (p.Glu539Ter)
HGVS:
  • NC_000019.10:g.48970958C>A
  • NG_012923.1:g.27396G>T
  • NM_001161587.2:c.1423G>T
  • NM_002103.5:c.1615G>TMANE SELECT
  • NP_001155059.1:p.Glu475Ter
  • NP_002094.2:p.Glu539Ter
  • NC_000019.9:g.49474215C>A
  • NM_002103.4:c.1615G>T
  • NR_027763.2:n.1630G>T
Protein change:
E475*
Links:
dbSNP: rs561646250
NCBI 1000 Genomes Browser:
rs561646250
Molecular consequence:
  • NR_027763.2:n.1630G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001161587.2:c.1423G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_002103.5:c.1615G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Glycogen storage disease 0, muscle (GSD0B)
Synonyms:
GSD 0b; Muscle glycogen synthase deficiency
Identifiers:
MONDO: MONDO:0012693; MedGen: C1969054; Orphanet: 137625; OMIM: 611556

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000819647Invitaecriteria provided, single submitter
Pathogenic
(Sep 17, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000819647.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change creates a premature translational stop signal (p.Glu539*) in the GYS1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs561646250, ExAC 0.001%). This variant has not been reported in the literature in individuals with GYS1-related disease. Loss-of-function variants in GYS1 are known to be pathogenic (PMID: 17928598, 19699667). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 13, 2021

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