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NM_000030.3(AGXT):c.26C>A (p.Thr9Asn)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 9, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000204016.8
Variation ID:
204016
Description:
single nucleotide variant
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NM_000030.3(AGXT):c.26C>A (p.Thr9Asn)

Allele ID
200420
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240868891 (GRCh38) GRCh38 UCSC
2: 241808308 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P21549:p.Thr9Asn
NC_000002.11:g.241808308C>A
NC_000002.12:g.240868891C>A
... more HGVS
Protein change
T9N
Other names
-
Canonical SPDI
NC_000002.12:240868890:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00379 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00670
The Genome Aggregation Database (gnomAD), exomes 0.00919
The Genome Aggregation Database (gnomAD) 0.00787
Trans-Omics for Precision Medicine (TOPMed) 0.00682
1000 Genomes Project 0.00379
Exome Aggregation Consortium (ExAC) 0.01121
Links
ClinGen: CA275540
UniProtKB: P21549#VAR_060547
dbSNP: rs115014558
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 4 criteria provided, multiple submitters, no conflicts May 28, 2019 RCV000186218.4
Benign 2 criteria provided, multiple submitters, no conflicts Mar 28, 2016 RCV000314232.1
Benign 2 criteria provided, multiple submitters, no conflicts Dec 5, 2020 RCV001510634.4
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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
Benign
(Mar 28, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000538244.1
Submitted: (Apr 03, 2017)
Evidence details
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Benign
(Sep 17, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000331578.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type I
Allele origin: unknown
Mendelics
Accession: SCV001136272.1
Submitted: (Oct 22, 2019)
Evidence details
Likely benign
(Feb 13, 2018)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type I
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001299484.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (4)
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)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001717726.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Dec 04, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001843076.1
Submitted: (Sep 09, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28969594, 27884173, 15849466, 21228398, 20981092, 17495019)
Uncertain significance
(Nov 27, 2014)
no assertion criteria provided
Method: in vitro
Primary hyperoxaluria, type I
Allele origin: germline
Clinical Biochemistry Laboratory,Health Services Laboratory
Accession: SCV000239541.1
Submitted: (Nov 27, 2014)
Evidence details
Publications
PubMed (2)
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Primary hyperoxaluria type I
Allele origin: germline
Natera, Inc.
Accession: SCV001456044.1
Submitted: (Dec 28, 2020)
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: update and additional mutation analysis of the AGXT gene. Williams EL Human mutation 2009 PMID: 19479957
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
Intra-familial clinical heterogeneity: absence of genotype-phenotype correlation in primary hyperoxaluria type 1 in Israel. Frishberg Y American journal of nephrology 2005 PMID: 15961946
Implications of genotype and enzyme phenotype in pyridoxine response of patients with type I primary hyperoxaluria. Monico CG American journal of nephrology 2005 PMID: 15849466
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 rs115014558...

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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