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NM_000030.3(AGXT):c.65A>G (p.Asn22Ser) AND Primary hyperoxaluria, type I

Germline classification:
Benign (3 submissions)
Last evaluated:
Jan 13, 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:
RCV000186222.18

Allele description [Variation Report for NM_000030.3(AGXT):c.65A>G (p.Asn22Ser)]

NM_000030.3(AGXT):c.65A>G (p.Asn22Ser)

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.65A>G (p.Asn22Ser)
HGVS:
  • NC_000002.12:g.240868930A>G
  • NG_008005.1:g.5186A>G
  • NM_000030.3:c.65A>GMANE SELECT
  • NP_000021.1:p.Asn22Ser
  • NP_000021.1:p.Asn22Ser
  • NC_000002.11:g.241808347A>G
  • NM_000030.2:c.65A>G
  • P21549:p.Asn22Ser
Protein change:
N22S
Links:
UniProtKB: P21549#VAR_048236; dbSNP: rs34885252
NCBI 1000 Genomes Browser:
rs34885252
Molecular consequence:
  • NM_000030.3:c.65A>G - 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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000239546Clinical Biochemistry Laboratory, Health Services Laboratory
no assertion criteria provided
Uncertain significance
(Nov 27, 2014) 		germlineresearch

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000429357Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Benign
(Jan 13, 2018) 		germlineclinical testing

Citation Link,

SCV002076451Natera, Inc.
no assertion criteria provided
Benign
(Oct 17, 2019) 		germlineclinical testing

Help

Summary from all submissions

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

Citations

PubMed

Primary hyperoxaluria type 1: update and additional mutation analysis of the AGXT gene.

Williams EL, Acquaviva C, Amoroso A, Chevalier F, Coulter-Mackie M, Monico CG, Giachino D, Owen T, Robbiano A, Salido E, Waterham H, Rumsby G.

Hum Mutat. 2009 Jun;30(6):910-7. doi: 10.1002/humu.21021. Review.

PubMed [citation]
PMID:
19479957

Details of each submission

From Clinical Biochemistry Laboratory, Health Services Laboratory, SCV000239546.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000429357.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

From Natera, Inc., SCV002076451.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024