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NM_004130.4(GYG1):c.143+3G>C

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Apr 23, 2020)
Last evaluated:
Jan 3, 2020
Accession:
VCV000162661.3
Variation ID:
162661
Description:
single nucleotide variant
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NM_004130.4(GYG1):c.143+3G>C

Allele ID
172315
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q24
Genomic location
3: 148994280 (GRCh38) GRCh38 UCSC
3: 148712067 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_004130.3:c.143+3G>C
NC_000003.11:g.148712067G>C
NC_000003.12:g.148994280G>C
... more HGVS
Protein change
-
Other names
IVS2DS, G-C, +3
Canonical SPDI
NC_000003.12:148994279:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
The Genome Aggregation Database (gnomAD) 0.00016
Trans-Omics for Precision Medicine (TOPMed) 0.00018
1000 Genomes Project 0.00020
Links
ClinGen: CA175125
OMIM: 603942.0003
dbSNP: rs370652040
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Jul 14, 2017 RCV000387284.2
Pathogenic 1 criteria provided, single submitter Jan 3, 2020 RCV001054146.1
Pathogenic 1 criteria provided, single submitter Sep 17, 2019 RCV001090151.1
Pathogenic 1 no assertion criteria provided Dec 1, 2014 RCV000150098.4

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GYG1 - - GRCh38
GRCh37
97 111

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 14, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000329983.5
Submitted: (Nov 28, 2017)
Evidence details
Comment:
The c.143+3 G>C splice site variant in the GYG1 gene has been previously reported in association with polyglucoasen body myopathy in several unrelated individuals who … (more)
Pathogenic
(Jan 03, 2020)
criteria provided, single submitter
Method: clinical testing
Polyglucosan body myopathy 2
Glycogen storage disease XV
Allele origin: germline
Invitae
Accession: SCV001218447.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change falls in intron 2 of the GYG1 gene. It does not directly change the encoded amino acid sequence of the GYG1 protein, … (more)
Pathogenic
(Sep 17, 2019)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease XV
(Autosomal recessive inheritance)
Allele origin: unknown
Undiagnosed Diseases Network,NIH
Accession: SCV001245599.1
Submitted: (Apr 23, 2020)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Dec 01, 2014)
no assertion criteria provided
Method: literature only
POLYGLUCOSAN BODY MYOPATHY 2
Allele origin: germline
OMIM
Accession: SCV000196922.2
Submitted: (Jan 26, 2015)
Evidence details
Publications
PubMed (1)

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
Clinical heterogeneity and phenotype/genotype findings in 5 families with <i>GYG1</i> deficiency. Ben Yaou R Neurology. Genetics 2017 PMID: 29264399
Late-onset polyglucosan body myopathy in five patients with a homozygous mutation in GYG1. Akman HO Neuromuscular disorders : NMD 2016 PMID: 26652229
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
A new muscle glycogen storage disease associated with glycogenin-1 deficiency. Malfatti E Annals of neurology 2014 PMID: 25272951

Text-mined citations for rs370652040...

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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