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NM_000152.5(GAA):c.2105G>C (p.Arg702Pro)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Aug 30, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000593593.3
Variation ID:
593593
Description:
single nucleotide variant
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NM_000152.5(GAA):c.2105G>C (p.Arg702Pro)

Allele ID
584657
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80113282 (GRCh38) GRCh38 UCSC
17: 78087081 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.78087081G>C
NC_000017.11:g.80113282G>C
NG_009822.1:g.16727G>C
... more HGVS
Protein change
R702P
Other names
-
Canonical SPDI
NC_000017.11:80113281:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs398123172
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Aug 16, 2017 RCV000728685.1
Uncertain significance 1 criteria provided, single submitter Jul 1, 2019 RCV001193012.1
Likely pathogenic 1 criteria provided, single submitter Jul 22, 2021 RCV001585686.1
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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
Likely pathogenic
(Aug 16, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000856289.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jul 01, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001361536.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: GAA c.2105G>C (p.Arg702Pro) affects a highly conserved nucleotide and results in a non-conservative amino acid change in the encoded protein sequence. Five of … (more)
Likely pathogenic
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001810642.1
Submitted: (Aug 30, 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
Repository of mutations from Oman: The entry point to a national mutation database. Rajab A F1000Research 2015 PMID: 26594346
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAA - - - -

Text-mined citations for rs398123172...

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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 27, 2021