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NM_000030.3(AGXT):c.466G>A (p.Gly156Arg)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
4 (Most recent: Nov 23, 2016)
Last evaluated:
Jan 14, 2016
Accession:
VCV000005650.1
Variation ID:
5650
Description:
single nucleotide variant
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NM_000030.3(AGXT):c.466G>A (p.Gly156Arg)

Allele ID
20689
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240871391 (GRCh38) GRCh38 UCSC
2: 241810808 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P21549:p.Gly156Arg
NC_000002.11:g.241810808G>A
NC_000002.12:g.240871391G>A
... more HGVS
Protein change
G156R
Other names
AGXT, GLY158ARG
Canonical SPDI
NC_000002.12:240871390:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00003
Exome Aggregation Consortium (ExAC) 0.00004
Links
ClinGen: CA340448
UniProtKB: P21549#VAR_010972
OMIM: 604285.0012
dbSNP: rs121908530
Varsome
Comment on variant
NCBI staff reviewed the sequence information reported in PubMed 10453743 to determine the location of this allele on current reference sequence.
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, single submitter Jan 14, 2016 RCV000006004.4
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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
459 562

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 14, 2016)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type I
Allele origin: unknown
Counsyl
Accession: SCV000485589.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (5)
Pathogenic
(Jun 01, 1999)
no assertion criteria provided
Method: literature only
HYPEROXALURIA, PRIMARY, TYPE I
Allele origin: germline
OMIM
Accession: SCV000026186.1
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
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: SCV000239643.1
Submitted: (Nov 27, 2014)
Evidence details
Publications
PubMed (2)
Pathogenic
(Jul 17, 2014)
no assertion criteria provided
Method: literature only
Primary hyperoxaluria, type I
Allele origin: germline
GeneReviews
Accession: SCV000172453.2
Submitted: (Jul 24, 2014)
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
Primary Hyperoxaluria Type 1 Milliner DS - 2017 PMID: 20301460
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
Mutation spectrum of primary hyperoxaluria type 1 in Tunisia: implication for diagnosis in North Africa. Nagara M Gene 2013 PMID: 23810941
Selected exonic sequencing of the AGXT gene provides a genetic diagnosis in 50% of patients with primary hyperoxaluria type 1. Williams E Clinical chemistry 2007 PMID: 17495019
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
Consequences of missense mutations for dimerization and turnover of alanine:glyoxylate aminotransferase: study of a spectrum of mutations. Coulter-Mackie MB Molecular genetics and metabolism 2006 PMID: 16971151
Primary hyperoxaluria type I: a model for multiple mutations in a monogenic disease within a distinct ethnic group. Rinat C Journal of the American Society of Nephrology : JASN 1999 PMID: 10541294
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
http://www.uclh.nhs.uk/OurServices/ServiceA-Z/PATH/PATHBIOMED/CBIO/Documents/AGXT%20mutation%20database.pdf - - - -

Text-mined citations for rs121908530...

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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 Oct 16, 2021