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NM_000030.3(AGXT):c.346G>A (p.Gly116Arg)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 13, 2019
Accession:
VCV000189021.4
Variation ID:
189021
Description:
single nucleotide variant
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NM_000030.3(AGXT):c.346G>A (p.Gly116Arg)

Allele ID
186655
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240869350 (GRCh38) GRCh38 UCSC
2: 241808767 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P21549:p.Gly116Arg
NC_000002.11:g.241808767G>A
NC_000002.12:g.240869350G>A
... more HGVS
Protein change
G116R
Other names
-
Canonical SPDI
NC_000002.12:240869349:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00013
The Genome Aggregation Database (gnomAD), exomes 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA274270
UniProtKB: P21549#VAR_010971
dbSNP: rs180177207
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Dec 30, 2017 RCV000169408.3
Likely pathogenic 1 criteria provided, single submitter Sep 13, 2019 RCV001236818.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
AGXT - - GRCh38
GRCh37
450 553

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Oct 16, 2014)
criteria provided, single submitter
Method: literature only
Primary hyperoxaluria, type I
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220811.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (5)
Likely pathogenic
(Sep 13, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001409555.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces glycine with arginine at codon 116 of the AGXT protein (p.Gly116Arg). The glycine residue is weakly conserved and there is a … (more)
Likely pathogenic
(Dec 30, 2017)
criteria provided, single submitter
Method: curation
Primary hyperoxaluria, type I
Allele origin: unknown
Department of Genetics,Sultan Qaboos University Hospital, Oman
Accession: SCV000891624.1
Submitted: (Oct 25, 2018)
Evidence details
Pathogenic
(Nov 27, 2014)
no assertion criteria provided
Method: in vitro
Primary hyperoxaluria, type I
Allele origin: germline
Clinical Biochemistry Laboratory,Health Services Laboratory
Accession: SCV000239632.1
Submitted: (Nov 27, 2014)
Evidence details
Publications
PubMed (1)

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
Left Lateral Sectionectomy of the Native Liver and Combined Living-Related Liver-Kidney Transplantation for Primary Hyperoxaluria Type 1. Chen GY Medicine 2015 PMID: 26252291
Performance evaluation of Sanger sequencing for the diagnosis of primary hyperoxaluria and comparison with targeted next generation sequencing. Williams EL Molecular genetics & genomic medicine 2015 PMID: 25629080
Data from a large European study indicate that the outcome of primary hyperoxaluria type 1 correlates with the AGXT mutation type. Mandrile G Kidney international 2014 PMID: 24988064
Comprehensive mutation screening in 55 probands with type 1 primary hyperoxaluria shows feasibility of a gene-based diagnosis. Monico CG Journal of the American Society of Nephrology : JASN 2007 PMID: 17460142
AGXT gene mutations and their influence on clinical heterogeneity of type 1 primary hyperoxaluria. Amoroso A Journal of the American Society of Nephrology : JASN 2001 PMID: 11562405
Molecular analysis of hyperoxaluria type 1 in Italian patients reveals eight new mutations in the alanine: glyoxylate aminotransferase gene. Pirulli D Human genetics 1999 PMID: 10453743
Gene symbol: AGXT. Disease: primary hyperoxaluria type I. Amoroso A Human genetics 1999 PMID: 10394939
http://www.uclh.nhs.uk/OurServices/ServiceA-Z/PATH/PATHBIOMED/CBIO/Documents/AGXT%20mutation%20database.pdf - - - -

Text-mined citations for rs180177207...

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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 18, 2021