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NM_000030.3(AGXT):c.866G>A (p.Arg289His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000198982.5
Variation ID:
198982
Description:
single nucleotide variant
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NM_000030.3(AGXT):c.866G>A (p.Arg289His)

Allele ID
196142
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240877556 (GRCh38) GRCh38 UCSC
2: 241816973 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.241816973G>A
NC_000002.12:g.240877556G>A
NG_008005.1:g.13812G>A
NM_000030.3:c.866G>A MANE Select NP_000021.1:p.Arg289His missense
Protein change
R289H
Other names
-
Canonical SPDI
NC_000002.12:240877555:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00124
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00076
Exome Aggregation Consortium (ExAC) 0.00143
The Genome Aggregation Database (gnomAD), exomes 0.00098
1000 Genomes Project 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00140
Links
ClinGen: CA247930
dbSNP: rs61729604
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 criteria provided, multiple submitters, no conflicts Dec 19, 2017 RCV000186341.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 8, 2020 RCV000587981.5
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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
Uncertain significance
(Jun 26, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000693981.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The AGXT c.866G>A (p.Arg289His) variant involves the alteration of a non-conserved nucleotide and is predicted to be benign by 2/3 in silico tools. … (more)
Uncertain significance
(Dec 19, 2017)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type I
Allele origin: unknown
Counsyl
Accession: SCV000800738.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type I
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001297137.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Mar 30, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232896.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001110251.3
Submitted: (Jan 07, 2021)
Evidence details
Pathogenic
(Nov 27, 2014)
no assertion criteria provided
Method: research
Primary hyperoxaluria, type I
Allele origin: germline
Clinical Biochemistry Laboratory,Health Services Laboratory
Accession: SCV000239687.1
Submitted: (Nov 27, 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
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
Primary hyperoxaluria type 1: update and additional mutation analysis of the AGXT gene. Williams EL Human mutation 2009 PMID: 19479957
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=AGXT - - - -
http://www.uclh.nhs.uk/OurServices/ServiceA-Z/PATH/PATHBIOMED/CBIO/Documents/AGXT%20mutation%20database.pdf - - - -

Text-mined citations for rs61729604...

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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