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NM_005609.4(PYGM):c.2392T>C (p.Trp798Arg)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 12, 2020
Accession:
VCV000002312.5
Variation ID:
2312
Description:
single nucleotide variant
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NM_005609.4(PYGM):c.2392T>C (p.Trp798Arg)

Allele ID
17351
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.1
Genomic location
11: 64746796 (GRCh38) GRCh38 UCSC
11: 64514268 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_100:g.3661T>C
P11217:p.Trp798Arg
NC_000011.9:g.64514268A>G
... more HGVS
Protein change
W798R, W710R
Other names
W797R
NM_001164716.1(PYGM):c.2128T>C(p.Trp710Arg)
NM_005609.2(PYGM):c.2392T>C(p.Trp798Arg)
Canonical SPDI
NC_000011.10:64746795:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA222889
UniProtKB: P11217#VAR_014015
OMIM: 608455.0015
dbSNP: rs119103258
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 7 criteria provided, multiple submitters, no conflicts Jun 12, 2020 RCV000002402.9
Pathogenic 2 criteria provided, multiple submitters, no conflicts Sep 26, 2016 RCV000081312.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PYGM - - GRCh38
GRCh37
603 614

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 11, 2012)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000227678.5
Submitted: (Jun 30, 2017)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Jul 29, 2015)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type V
Allele origin: unknown
Counsyl
Accession: SCV000677925.1
Submitted: (Jun 22, 2017)
Evidence details
Publications
PubMed (5)
Likely pathogenic
(May 31, 2018)
criteria provided, single submitter
Method: curation
Glycogen storage disease, type V
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV000803466.1
Submitted: (Jun 13, 2018)
Evidence details
Publications
PubMed (4)
Comment:
This variant is interpreted as a Likely Pathogenic, for Glycogen storage disease 5, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PM2 => … (more)
Likely pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type V
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893903.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Sep 26, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000491226.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The W798R variant in the PYGM gene has been reported previously, sometimes with alternate nomenclature of W797R, in the homozygous state, as well as the … (more)
Pathogenic
(Jun 12, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type V
Allele origin: germline
Invitae
Accession: SCV001580144.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change replaces tryptophan with arginine at codon 798 of the PYGM protein (p.Trp798Arg). The tryptophan residue is highly conserved and there is a … (more)
Pathogenic
(Jun 26, 2014)
no assertion criteria provided
Method: literature only
Glycogen storage disease, type V
Allele origin: germline
GeneReviews
Accession: SCV000172201.2
Submitted: (Jul 09, 2014)
Evidence details
Publications
PubMed (3)
Pathogenic
(Jan 01, 2001)
no assertion criteria provided
Method: literature only
MCARDLE DISEASE
Allele origin: germline
OMIM
Accession: SCV000022560.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease V
Allele origin: germline
Natera, Inc.
Accession: SCV001461268.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Single-centre experience on genotypic and phenotypic features of southern Brazilian patients with McArdle disease. Lorenzoni PJ Acta neurologica Belgica 2020 PMID: 30415384
Glycogen Storage Disease Type V Martín MA - 2019 PMID: 20301518
Genotypic and phenotypic features of all Spanish patients with McArdle disease: a 2016 update. Santalla A BMC genomics 2017 PMID: 29143597
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Genotypic and phenotypic features of McArdle disease: insights from the Spanish national registry. Lucia A Journal of neurology, neurosurgery, and psychiatry 2012 PMID: 22250184
Expression of the muscle glycogen phosphorylase gene in patients with McArdle disease: the role of nonsense-mediated mRNA decay. Nogales-Gadea G Human mutation 2008 PMID: 17994553
A proposed molecular diagnostic flowchart for myophosphorylase deficiency (McArdle disease) in blood samples from Spanish patients. Rubio JC Human mutation 2007 PMID: 17221871
CBS domains form energy-sensing modules whose binding of adenosine ligands is disrupted by disease mutations. Scott JW The Journal of clinical investigation 2004 PMID: 14722619
Molecular heterogeneity of myophosphorylase deficiency (McArdle's disease): a genotype-phenotype correlation study. Martín MA Annals of neurology 2001 PMID: 11706962
Resolution of a mispaired secondary structure intermediate could account for a novel micro-insertion/deletion (387 insA/del 8 bp) in the PYGM gene causing McArdle's disease. Martín MA Clinical genetics 2001 PMID: 11168025
A novel missense mutation (W797R) in the myophosphorylase gene in Spanish patients with McArdle disease. Fernández R Archives of neurology 2000 PMID: 10681080
A missense mutation W797R in the myophosphorylase gene in a Spanish patient with McArdle's disease. Rubio JC Muscle & nerve 2000 PMID: 10590419
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PYGM - - - -

Text-mined citations for rs119103258...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 24, 2021