NM_000030.3(AGXT):c.705G>A (p.Thr235=) AND Primary hyperoxaluria, type I

Clinical significance:Benign (Last evaluated: Jan 13, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000186252.3

Allele description [Variation Report for NM_000030.3(AGXT):c.705G>A (p.Thr235=)]

NM_000030.3(AGXT):c.705G>A (p.Thr235=)

Gene:
AGXT:alanine--glyoxylate and serine--pyruvate aminotransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q37.3
Genomic location:
Preferred name:
NM_000030.3(AGXT):c.705G>A (p.Thr235=)
HGVS:
  • NC_000002.12:g.240875133G>A
  • NG_008005.1:g.11389G>A
  • NM_000030.3:c.705G>AMANE SELECT
  • NP_000021.1:p.Thr235=
  • NC_000002.11:g.241814550G>A
  • NM_000030.2:c.705G>A
  • NP_000021.1:p.Thr235Thr
  • NP_000021.1:p.Thr235Thr
Links:
dbSNP: rs35977912
NCBI 1000 Genomes Browser:
rs35977912
Molecular consequence:
  • NM_000030.3:c.705G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000239576Clinical Biochemistry Laboratory,Health Services Laboratoryno assertion criteria providedUncertain significance
(Nov 27, 2014)
germlineresearch

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

Citation Link,

SCV000429368Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV001456051Natera, Inc.no assertion criteria providedBenign
(Sep 16, 2020)
germlineclinical testing

Summary from all submissions

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

Citations

PubMed

The major allele of the alanine:glyoxylate aminotransferase gene: nine novel mutations and polymorphisms associated with primary hyperoxaluria type 1.

Coulter-Mackie MB, Lian Q, Applegarth D, Toone J.

Mol Genet Metab. 2005 Sep-Oct;86(1-2):172-8. Epub 2005 Jun 15.

PubMed [citation]
PMID:
15963748

Details of each submission

From Clinical Biochemistry Laboratory,Health Services Laboratory, SCV000239576.1

#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 Clinical Services Laboratory,Illumina, SCV000429368.3

#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., SCV001456051.1

#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: Sep 18, 2021

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