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NM_000030.3(AGXT):c.731T>C (p.Ile244Thr) AND AGXT-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 5, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003407286.6

Allele description [Variation Report for NM_000030.3(AGXT):c.731T>C (p.Ile244Thr)]

NM_000030.3(AGXT):c.731T>C (p.Ile244Thr)

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.731T>C (p.Ile244Thr)
HGVS:
  • NC_000002.12:g.240875159T>C
  • NG_008005.1:g.11415T>C
  • NM_000030.3:c.731T>CMANE SELECT
  • NP_000021.1:p.Ile244Thr
  • NP_000021.1:p.Ile244Thr
  • NC_000002.11:g.241814576T>C
  • NM_000030.2:c.731T>C
  • P21549:p.Ile244Thr
Protein change:
I244T; ILE244THR
Links:
UniProtKB: P21549#VAR_008881; OMIM: 604285.0007; dbSNP: rs121908525
NCBI 1000 Genomes Browser:
rs121908525
Molecular consequence:
  • NM_000030.3:c.731T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
AGXT-related disorder
Synonyms:
AGXT-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004110893PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Dec 5, 2023) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004110893.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The AGXT c.731T>C variant is predicted to result in the amino acid substitution p.Ile244Thr. This variant has been reported in the homozygous or compound heterozygous state in many individuals with primary hyperoxaluria type 1 and is one of the most frequent causative variants (Mandrile et al. 2014. PubMed ID: 24988064; Ahmed et al. 2022. PubMed ID: 35661454; Monico et al. 2007. PubMed ID: 17460142; Rhuma et al. 2018. PubMed ID: 29456205). A large Libyan cohort study of individuals with primary hyperoxaluria type 1 indicated this was a founder variant in this population (Rhuma et al. 2018. PubMed ID: 29456205). Of note, the p.Ile244Thr variant is many times observed with a common variant, c.32C>T p.Pro11Leu. Functional studies indicate that the Pro11Leu variant modifies the effect of the p.Ile244Thr and reduces protein activity and localization (Santana et al. 2003. PubMed ID: 12777626 ; Fargue et al. 2013. PubMed ID: 23229545; Dindo et al. 2017. PubMed ID: 28906061). This variant is reported in 0.028% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-241814576-T-C). This variant is interpreted as pathogenic for autosomal recessive AGXT-related disorders.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 18, 2024