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NM_000152.5(GAA):c.1920T>G (p.Pro640=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Aug 30, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000255358.9
Variation ID:
255358
Description:
single nucleotide variant
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NM_000152.5(GAA):c.1920T>G (p.Pro640=)

Allele ID
256527
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80112907 (GRCh38) GRCh38 UCSC
17: 78086706 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_673t1:c.1920T>G
LRG_673:g.16352T>G
NC_000017.10:g.78086706T>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:80112906:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00026
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00017
The Genome Aggregation Database (gnomAD), exomes 0.00018
Exome Aggregation Consortium (ExAC) 0.00032
Links
ClinGen: CA8815546
dbSNP: rs144090460
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 18, 2017 RCV000243841.4
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jan 1, 2021 RCV000675235.4
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Jul 22, 2021 RCV001079385.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAA - - GRCh38
GRCh37
1479 1518

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000302671.1
Submitted: (Apr 28, 2016)
Evidence details
Uncertain significance
(Nov 11, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000337540.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Aug 18, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000721670.1
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
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001287879.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
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
(Nov 17, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV000752097.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001502247.2
Submitted: (Jul 04, 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: SCV001810638.1
Submitted: (Aug 30, 2021)
Evidence details
Likely benign
(May 10, 2017)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000800881.1
Submitted: (May 23, 2018)
Evidence details
Uncertain significance
(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: SCV001423081.1
Submitted: (Mar 09, 2020)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.1920T>G (p.Pro640=) variant in GAA has not been reported in individuals with Glycogen Storage Disease II but has been reported in 2 European individuals … (more)

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
Development of a feasible assay for the detection of GAA mutations in patients with Pompe disease. Er TK Clinica chimica acta; international journal of clinical chemistry 2014 PMID: 24444888
Identification of eight novel mutations of the acid alpha-glucosidase gene causing the infantile or juvenile form of glycogen storage disease type II. Wan L Journal of neurology 2008 PMID: 18458862
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAA - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/f319b1ab-4ee7-406b-a3e3-84dfbddb64bf - - - -

Text-mined citations for rs144090460...

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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