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NM_000030.3(AGXT):c.335C>A (p.Ala112Asp) AND Primary hyperoxaluria

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 25, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV004586609.1

Allele description [Variation Report for NM_000030.3(AGXT):c.335C>A (p.Ala112Asp)]

NM_000030.3(AGXT):c.335C>A (p.Ala112Asp)

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.335C>A (p.Ala112Asp)
HGVS:
  • NC_000002.12:g.240869339C>A
  • NG_008005.1:g.5595C>A
  • NM_000030.3:c.335C>AMANE SELECT
  • NP_000021.1:p.Ala112Asp
  • NP_000021.1:p.Ala112Asp
  • NC_000002.11:g.241808756C>A
  • NM_000030.2:c.335C>A
  • P21549:p.Ala112Asp
Protein change:
A112D
Links:
UniProtKB: P21549#VAR_060550; dbSNP: rs796052061
NCBI 1000 Genomes Browser:
rs796052061
Molecular consequence:
  • NM_000030.3:c.335C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Primary hyperoxaluria
Identifiers:
MONDO: MONDO:0002474; MedGen: C0020501; OMIM: PS259900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005076440Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Apr 25, 2024) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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Summary from all submissions

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

Citations

PubMed

The AGT gene in Africa: a distinctive minor allele haplotype, a polymorphism (V326I), and a novel PH1 mutation (A112D) in Black Africans.

Coulter-Mackie MB, Tung A, Henderson HE, Toone JR, Applegarth DA.

Mol Genet Metab. 2003 Jan;78(1):44-50.

PubMed [citation]
PMID:
12559847

Consequences of missense mutations for dimerization and turnover of alanine:glyoxylate aminotransferase: study of a spectrum of mutations.

Coulter-Mackie MB, Lian Q.

Mol Genet Metab. 2006 Dec;89(4):349-59. Epub 2006 Sep 12.

PubMed [citation]
PMID:
16971151

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005076440.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: AGXT c.335C>A (p.Ala112Asp) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 241646 control chromosomes (gnomAD). c.335C>A has been reported in the literature in individuals affected with Primary Hyperoxaluria Type 1 (Coulter-Mackie_2003). These data indicate that the variant is likely to be associated with disease. Publications also reported experimental evidence evaluating an impact on protein function, and demonstrated that the variant resulted in about ~2-5% of normal catalytic activity in both patient derived samples and in in vitro expression systems on the background of the major allele (Coulter-Mackie_2003, Coulter-Mackie_2006). The following publications have been ascertained in the context of this evaluation (PMID: 12559847, 16971151). ClinVar contains an entry for this variant (Variation ID: 204093). Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Jan 19, 2025