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NM_000152.5(GAA):c.1356C>T (p.Ala452=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Aug 30, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000286268.10
Variation ID:
286268
Description:
single nucleotide variant
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NM_000152.5(GAA):c.1356C>T (p.Ala452=)

Allele ID
270505
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80109974 (GRCh38) GRCh38 UCSC
17: 78083773 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_673t1:c.1356C>T
LRG_673:g.13419C>T
NC_000017.10:g.78083773C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:80109973:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00008
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00007
Trans-Omics for Precision Medicine (TOPMed) 0.00007
Links
ClinGen: CA8815296
dbSNP: rs757893858
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Feb 27, 2018 RCV000725823.4
Likely benign 1 criteria provided, single submitter Dec 11, 2017 RCV000312644.3
Conflicting interpretations of pathogenicity 6 criteria provided, conflicting interpretations Jul 22, 2021 RCV001001227.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAA - - GRCh38
GRCh37
1499 1538

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Feb 16, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000339627.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 11, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000717256.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Uncertain significance
(Feb 27, 2018)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Blueprint Genetics
Accession: SCV000927550.1
Submitted: (May 08, 2019)
Comment:
Patient analyzed with Hypertrophic Cardiomyopathy (HCM) Panel
Evidence details
Likely benign
(May 03, 2019)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001158390.1
Submitted: (Aug 05, 2019)
Evidence details
Uncertain significance
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001282567.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV001043667.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001810598.1
Submitted: (Aug 30, 2021)
Evidence details
Likely benign
(Jan 22, 2020)
no assertion criteria provided
Method: curation
Glycogen storage disease, type II
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001422896.1
Submitted: (Mar 09, 2020)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.1356C>T (p.Ala452=) variant in GAA has not been previously reported in individuals with Glycogen Storage Disease II but has been reported as a VUS … (more)
Uncertain significance
(Jan 24, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type II
Allele origin: germline
Natera, Inc.
Accession: SCV001453426.1
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.

Text-mined citations for rs757893858...

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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 07, 2021