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NM_000030.3(AGXT):c.322T>C (p.Trp108Arg)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Jan 16, 2020
Accession:
VCV000188891.5
Variation ID:
188891
Description:
single nucleotide variant
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NM_000030.3(AGXT):c.322T>C (p.Trp108Arg)

Allele ID
186654
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 240869326 (GRCh38) GRCh38 UCSC
2: 241808743 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P21549:p.Trp108Arg
NC_000002.11:g.241808743T>C
NC_000002.12:g.240869326T>C
... more HGVS
Protein change
W108R
Other names
-
Canonical SPDI
NC_000002.12:240869325:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00000
Links
ClinGen: CA274089
UniProtKB: P21549#VAR_060549
dbSNP: rs180177197
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, single submitter Jul 19, 2014 RCV000169249.4
Pathogenic 1 criteria provided, single submitter Jan 16, 2020 RCV000812967.3
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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
(Jul 19, 2014)
criteria provided, single submitter
Method: literature only
Primary hyperoxaluria, type I
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220531.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (11)
Pathogenic
(Jan 16, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000953297.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change replaces tryptophan with arginine at codon 108 of the AGXT protein (p.Trp108Arg). The tryptophan residue is highly conserved and there is a … (more)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Primary hyperoxaluria type I
Allele origin: germline
Natera, Inc.
Accession: SCV001456046.1
Submitted: (Dec 28, 2020)
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: SCV000239625.1
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
Mutational Analysis of Agxt in Tunisian Population with Primary Hyperoxaluria Type 1. M'dimegh S Annals of human genetics 2017 PMID: 27935012
Allele-specific characterization of alanine: glyoxylate aminotransferase variants associated with primary hyperoxaluria. Lage MD PloS one 2014 PMID: 24718375
Rapid profiling of disease alleles using a tunable reporter of protein misfolding. Pittman AM Genetics 2012 PMID: 22923379
Biochemical analyses are instrumental in identifying the impact of mutations on holo and/or apo-forms and on the region(s) of alanine:glyoxylate aminotransferase variants associated with primary hyperoxaluria type I. Oppici E Molecular genetics and metabolism 2012 PMID: 22018727
Partial trypsin digestion as an indicator of mis-folding of mutant alanine:glyoxylate aminotransferase and chaperone effects of specific ligands. Study of a spectrum of missense mutants. Coulter-Mackie MB Molecular genetics and metabolism 2008 PMID: 18448374
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
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
Genetic heterogeneity in primary hyperoxaluria type 1: impact on diagnosis. Coulter-Mackie MB Molecular genetics and metabolism 2004 PMID: 15464418
Primary hyperoxaluria: genotype-phenotype correlation. Pirulli D Journal of nephrology 2003 PMID: 12768081
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
Identification of new mutations in primary hyperoxaluria type 1 (PH1). von Schnakenburg C Journal of nephrology 1998 PMID: 9604803
http://www.uclh.nhs.uk/OurServices/ServiceA-Z/PATH/PATHBIOMED/CBIO/Documents/AGXT%20mutation%20database.pdf - - - -

Text-mined citations for rs180177197...

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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