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NM_002863.5(PYGL):c.1768+1G>A

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Feb 21, 2021)
Last evaluated:
Jul 27, 2020
Accession:
VCV000011992.4
Variation ID:
11992
Description:
single nucleotide variant
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NM_002863.5(PYGL):c.1768+1G>A

Allele ID
27031
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q22.1
Genomic location
14: 50912155 (GRCh38) GRCh38 UCSC
14: 51378873 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000014.8:g.51378873C>T
NC_000014.9:g.50912155C>T
NG_012796.1:g.37376G>A
... more HGVS
Protein change
-
Other names
IVS14DS, G-A, +1
Canonical SPDI
NC_000014.9:50912154:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00004
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA341169
OMIM: 613741.0001
dbSNP: rs113993982
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 5 criteria provided, multiple submitters, no conflicts Jul 27, 2020 RCV000012772.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PYGL - - GRCh38
GRCh37
201 218

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Apr 13, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VI
Allele origin: germline
Invitae
Accession: SCV000819606.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 14 of the PYGL gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VI
Allele origin: germline
Pathology and Clinical Laboratory Medicine,King Fahad Medical City
Accession: SCV000996283.1
Submitted: (Jun 18, 2019)
Evidence details
Pathogenic
(Jul 27, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VI
Allele origin: unknown
Baylor Genetics
Accession: SCV001522876.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
pathologic
(May 17, 2011)
no assertion criteria provided
Method: curation
Glycogen Storage Disease Type VI
Allele origin: not provided
GeneReviews
Accession: SCV000040944.1
Submitted: (Jan 08, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.
Pathogenic
(Apr 01, 1998)
no assertion criteria provided
Method: literature only
GLYCOGEN STORAGE DISEASE VI
Allele origin: germline
OMIM
Accession: SCV000033007.2
Submitted: (Dec 30, 2010)
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
Glycogen Storage Disease Type VI Labrador E - 2019 PMID: 20301760
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Liver glycogen storage diseases due to phosphorylase system deficiencies: diagnosis thanks to non invasive blood enzymatic and molecular studies. Davit-Spraul A Molecular genetics and metabolism 2011 PMID: 21646031
Identification of a mutation in liver glycogen phosphorylase in glycogen storage disease type VI. Chang S Human molecular genetics 1998 PMID: 9536091
Mutations in the liver glycogen phosphorylase gene (PYGL) underlying glycogenosis type VI. Burwinkel B American journal of human genetics 1998 PMID: 9529348

Text-mined citations for rs113993982...

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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 Sep 29, 2021