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NM_000152.5(GAA):c.59C>G (p.Ser20Cys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 9, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000427881.1

Allele description [Variation Report for NM_000152.5(GAA):c.59C>G (p.Ser20Cys)]

NM_000152.5(GAA):c.59C>G (p.Ser20Cys)

Gene:
GAA:alpha glucosidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_000152.5(GAA):c.59C>G (p.Ser20Cys)
HGVS:
  • NC_000017.11:g.80104645C>G
  • NG_009822.1:g.8090C>G
  • NM_000152.5:c.59C>GMANE SELECT
  • NM_001079803.3:c.59C>G
  • NM_001079804.3:c.59C>G
  • NP_000143.2:p.Ser20Cys
  • NP_001073271.1:p.Ser20Cys
  • NP_001073272.1:p.Ser20Cys
  • LRG_673t1:c.59C>G
  • LRG_673:g.8090C>G
  • NC_000017.10:g.78078444C>G
  • NM_000152.3:c.59C>G
Protein change:
S20C
Links:
dbSNP: rs752449306
NCBI 1000 Genomes Browser:
rs752449306
Molecular consequence:
  • NM_000152.5:c.59C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079803.3:c.59C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079804.3:c.59C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000535010GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 9, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000535010.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The S20C variant in the GAA gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The S20C variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The S20C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is not conserved. In silico analysis predicts this variant likely does not alter the protein structure/function. We interpret S20C as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024