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NM_000030.3(AGXT):c.1084G>A (p.Gly362Ser) AND Primary hyperoxaluria

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 19, 2018
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:
RCV000780822.1

Allele description [Variation Report for NM_000030.3(AGXT):c.1084G>A (p.Gly362Ser)]

NM_000030.3(AGXT):c.1084G>A (p.Gly362Ser)

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.1084G>A (p.Gly362Ser)
HGVS:
  • NC_000002.12:g.240878726G>A
  • NG_008005.1:g.14982G>A
  • NM_000030.3:c.1084G>AMANE SELECT
  • NP_000021.1:p.Gly362Ser
  • NC_000002.11:g.241818143G>A
  • NM_000030.2:c.1084G>A
Protein change:
G362S
Links:
dbSNP: rs569643246
NCBI 1000 Genomes Browser:
rs569643246
Molecular consequence:
  • NM_000030.3:c.1084G>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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000918405Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Nov 19, 2018) 		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

Phenotype-Genotype Correlations and Estimated Carrier Frequencies of Primary Hyperoxaluria.

Hopp K, Cogal AG, Bergstralh EJ, Seide BM, Olson JB, Meek AM, Lieske JC, Milliner DS, Harris PC; Rare Kidney Stone Consortium..

J Am Soc Nephrol. 2015 Oct;26(10):2559-70. doi: 10.1681/ASN.2014070698. Epub 2015 Feb 2.

PubMed [citation]
PMID:
25644115
PMCID:
PMC4587693

Data from a large European study indicate that the outcome of primary hyperoxaluria type 1 correlates with the AGXT mutation type.

Mandrile G, van Woerden CS, Berchialla P, Beck BB, Acquaviva Bourdain C, Hulton SA, Rumsby G; OxalEurope Consortium..

Kidney Int. 2014 Dec;86(6):1197-204. doi: 10.1038/ki.2014.222. Epub 2014 Jul 2.

PubMed [citation]
PMID:
24988064

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000918405.1

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

Description

Variant summary: AGXT c.1084G>A (p.Gly362Ser) results in a non-conservative amino acid change located in the Aminotransferase class V domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3e-05 in 167718 control chromosomes (gnomAD). c.1084G>A has been reported in the literature and in our internal testing experience in compound heterozygous individuals affected with Primary Hyperoxaluria Type 1 (Mandrile 2014, Oppici 2015, Internal testing). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Sep 29, 2024