NM_000030.3(AGXT):c.697C>T (p.Arg233Cys) AND Primary hyperoxaluria, type I

Germline classification:: Pathogenic/Likely pathogenic (7 submissions)
Last evaluated:: Mar 27, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000006001.22

Allele description [Variation Report for NM_000030.3(AGXT):c.697C>T (p.Arg233Cys)]

NM_000030.3(AGXT):c.697C>T (p.Arg233Cys)

Gene:

AGXT:alanine--glyoxylate aminotransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q37.3

Genomic location:

Preferred name:

NM_000030.3(AGXT):c.697C>T (p.Arg233Cys)

HGVS:

NC_000002.12:g.240875125C>T
NG_008005.1:g.11381C>T
NM_000030.3:c.697C>TMANE SELECT
NP_000021.1:p.Arg233Cys
NP_000021.1:p.Arg233Cys
NC_000002.11:g.241814542C>T
NM_000030.2:c.697C>T
P21549:p.Arg233Cys

Protein change:

R233C; ARG233CYS

Links:

UniProtKB: P21549#VAR_008879; OMIM: 604285.0008; dbSNP: rs121908526

NCBI 1000 Genomes Browser:

rs121908526

Molecular consequence:

NM_000030.3:c.697C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Primary hyperoxaluria, type I (HP1)
Synonyms:: OXALOSIS I; Primary hyperoxaluria type 1; Oxalosis 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009823; MedGen: C0268164; Orphanet: 416; Orphanet: 93598; OMIM: 259900

Recent activity

Clear Turn Off Turn On

Wnt4 [Drosophila guanche]
Wnt4 [Drosophila guanche]
Gene ID:117584445

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000026183	OMIM	no assertion criteria provided	Pathogenic (Jun 1, 1997)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000172456	GeneReviews	no classification provided	not provided	germline	literature only
SCV000239670	Clinical Biochemistry Laboratory, Health Services Laboratory	no assertion criteria provided	Pathogenic (Nov 27, 2014)	germline	in vitro	PubMed (2) [See all records that cite these PMIDs] 9192270, 17495019 Citation Link,
SCV001162945	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 27, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001456050	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV002060387	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Nov 3, 2021)	unknown	clinical testing	PubMed (6) [See all records that cite these PMIDs] 18282470, 25629080, 18448374, 10862087, 17495019, 18782763 Citation Link,
SCV002776118	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 17, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	literature only, in vitro
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Primary hyperoxaluria type 1: a cluster of new mutations in exon 7 of the AGXT gene.

von Schnakenburg C, Rumsby G.

J Med Genet. 1997 Jun;34(6):489-92.

PubMed [citation]

PMID:: 9192270
PMCID:: PMC1050973

Mutation-based diagnostic testing for primary hyperoxaluria type 1: survey of results.

Coulter-Mackie MB, Lian Q, Applegarth DA, Toone J, Waters PJ, Vallance H.

Clin Biochem. 2008 May;41(7-8):598-602. doi: 10.1016/j.clinbiochem.2008.01.018. Epub 2008 Feb 7.

PubMed [citation]

PMID:: 18282470

See all PubMed Citations (8)

Details of each submission

From OMIM, SCV000026183.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a patient with type I primary hyperoxaluria (259900), von Schnakenburg and Rumsby (1997) found a homozygous 819C-T transition in the AGXT gene that mutated codon 233 from arginine to cysteine (R233C). A mutation in the adjacent nucleotide, 820G-A, mutated the same codon from arginine to histidine (604285.0009).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneReviews, SCV000172456.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Biochemistry Laboratory, Health Services Laboratory, SCV000239670.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	in vitro	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001162945.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001456050.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV002060387.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

NM_000030.2(AGXT):c.697C>T(R233C) is a missense variant classified as likely pathogenic in the context of primary hyperoxaluria type 1. R233C has been observed in cases with relevant disease (PMID: 10862087, 18282470, 25629080). Functional assessments of this variant are available in the literature (PMID: 18782763, 17495019, 18448374). Internal structural analysis of the variant is supportive of pathogenicity. R233C has been observed in population frequency databases (gnomAD: AFR 0.04%). In summary, NM_000030.2(AGXT):c.697C>T(R233C) is a missense variant that has internal structural support for pathogenicity and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002776118.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

Relating variation to medicine