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NM_000152.5(GAA):c.1634C>T (p.Pro545Leu)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
3 (Most recent: Nov 19, 2021)
Last evaluated:
Apr 30, 2020
Accession:
VCV000004032.4
Variation ID:
4032
Description:
single nucleotide variant
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NM_000152.5(GAA):c.1634C>T (p.Pro545Leu)

Allele ID
19071
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80111023 (GRCh38) GRCh38 UCSC
17: 78084822 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P10253:p.Pro545Leu
LRG_673t1:c.1634C>T LRG_673p1:p.Pro545Leu
NG_009822.1:g.14468C>T
... more HGVS
Protein change
P545L
Other names
-
Canonical SPDI
NC_000017.11:80111022:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA116616
UniProtKB: P10253#VAR_004297
OMIM: 606800.0013
dbSNP: rs121907942
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 Apr 30, 2020 RCV001174962.1
Pathogenic 1 no assertion criteria provided Dec 1, 1994 RCV000004247.4
Pathogenic 1 no assertion criteria provided Oct 12, 2021 RCV001785449.1
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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
1547 1587

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Apr 30, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001338444.1
Submitted: (May 13, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: GAA c.1634C>T (p.Pro545Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging … (more)
Pathogenic
(Dec 01, 1994)
no assertion criteria provided
Method: literature only
GLYCOGEN STORAGE DISEASE II, ADULT FORM
Allele origin: germline
OMIM
Accession: SCV000024413.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Pathogenic
(Oct 12, 2021)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002021171.1
Submitted: (Nov 19, 2021)
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
Childhood Pompe disease: clinical spectrum and genotype in 31 patients. van Capelle CI Orphanet journal of rare diseases 2016 PMID: 27189384
The pharmacological chaperone 1-deoxynojirimycin increases the activity and lysosomal trafficking of multiple mutant forms of acid alpha-glucosidase. Flanagan JJ Human mutation 2009 PMID: 19862843
Adult-onset glycogen storage disease type II: phenotypic and allelic heterogeneity in German patients. Vorgerd M Neurogenetics 1998 PMID: 10737124
The effect of a single base pair deletion (delta T525) and a C1634T missense mutation (pro545leu) on the expression of lysosomal alpha-glucosidase in patients with glycogen storage disease type II. Hermans MM Human molecular genetics 1994 PMID: 7881422

Text-mined citations for rs121907942...

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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 Nov 28, 2021