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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Chain B, T-cell surface glycoprotein CD4
Chain B, T-cell surface glycoprotein CD4
gi|158429692|pdb|2QAD|B

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000239546	Clinical Biochemistry Laboratory, Health Services Laboratory	no assertion criteria provided	Uncertain significance (Nov 27, 2014)	germline	research	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000429357	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV002076451	Natera, Inc.	no assertion criteria provided	Benign (Oct 17, 2019)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000239546

Clinical Biochemistry Laboratory, Health Services Laboratory

no assertion criteria provided

Uncertain significance
(Nov 27, 2014)

germline

research

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

Citation Link,

SCV000429357

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV002076451

Natera, Inc.

no assertion criteria provided

Benign
(Oct 17, 2019)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV000429357.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002076451.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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