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NM_000030.3(AGXT):c.680+480_776+69delinsTGAGA AND Primary hyperoxaluria, type I

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 27, 2023
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:
RCV000186403.5

Allele description [Variation Report for NM_000030.3(AGXT):c.680+480_776+69delinsTGAGA]

NM_000030.3(AGXT):c.680+480_776+69delinsTGAGA

Gene:
AGXT:alanine--glyoxylate aminotransferase [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
2q37.3
Genomic location:
Preferred name:
NM_000030.3(AGXT):c.680+480_776+69delinsTGAGA
Other names:
exon 7 del
HGVS:
  • NC_000002.12:g.240874542_240875273delinsTGAGA
  • NG_008005.1:g.10798_11529delinsTGAGA
  • NM_000030.3:c.680+480_776+69delinsTGAGAMANE SELECT
  • NP_000021.1:p.Lys228_Met259del32
  • NC_000002.11:g.241813959_241814690delinsTGAGA
  • NC_000002.12:g.240874542_240875273del732insTGAGA
  • NM_000030.2:c.680+480_776+69delinsTGAGA
Links:
dbSNP: rs1553648931
NCBI 1000 Genomes Browser:
rs1553648931
Molecular consequence:
  • NM_000030.3:c.680+480_776+69delinsTGAGA - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000030.3:c.680+480_776+69delinsTGAGA - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000239753Clinical Biochemistry Laboratory, Health Services Laboratory
no assertion criteria provided
Pathogenic
(Nov 27, 2014) 		germlineresearch

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

Citation Link,

SCV004176767Thalassemia Center, San Luigi University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 27, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, research

Citations

PubMed

Novel human pathological mutations. Gene symbol: AGXT. Disease: hyperoxaluria.

Robbiano A, Mandrile G, De Marchi M, Beck B, Baasner A, Murer L, Benetti E, Giachino D.

Hum Genet. 2010 Apr;127(4):468. No abstract available.

PubMed [citation]
PMID:
21488232

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Clinical Biochemistry Laboratory, Health Services Laboratory, SCV000239753.1

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

From Thalassemia Center, San Luigi University Hospital, SCV004176767.1

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

Description

ACMG:PVS1 PM1 PM2 PM4

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

Last Updated: May 7, 2024