NM_000030.3(AGXT):c.322T>C (p.Trp108Arg) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jan 16, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000812967.3

Allele description [Variation Report for NM_000030.3(AGXT):c.322T>C (p.Trp108Arg)]

NM_000030.3(AGXT):c.322T>C (p.Trp108Arg)

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.322T>C (p.Trp108Arg)
HGVS:
  • NC_000002.12:g.240869326T>C
  • NG_008005.1:g.5582T>C
  • NM_000030.3:c.322T>CMANE SELECT
  • NP_000021.1:p.Trp108Arg
  • NP_000021.1:p.Trp108Arg
  • NP_000021.1:p.Trp108Arg
  • NC_000002.11:g.241808743T>C
  • NM_000030.2:c.322T>C
  • P21549:p.Trp108Arg
Protein change:
W108R
Links:
UniProtKB: P21549#VAR_060549; dbSNP: rs180177197
NCBI 1000 Genomes Browser:
rs180177197
Molecular consequence:
  • NM_000030.3:c.322T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000953297Invitaecriteria provided, single submitter
Pathogenic
(Jan 16, 2020)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Identification of new mutations in primary hyperoxaluria type 1 (PH1).

von Schnakenburg C, Rumsby G.

J Nephrol. 1998 Mar-Apr;11 Suppl 1:15-7.

PubMed [citation]
PMID:
9604803

Intra-familial clinical heterogeneity: absence of genotype-phenotype correlation in primary hyperoxaluria type 1 in Israel.

Frishberg Y, Rinat C, Shalata A, Khatib I, Feinstein S, Becker-Cohen R, Weismann I, Wanders RJ, Rumsby G, Roels F, Mandel H.

Am J Nephrol. 2005 May-Jun;25(3):269-75. Epub 2005 Jun 15.

PubMed [citation]
PMID:
15961946
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV000953297.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change replaces tryptophan with arginine at codon 108 of the AGXT protein (p.Trp108Arg). The tryptophan residue is highly conserved and there is a moderate physicochemical difference between tryptophan and arginine. This variant is present in population databases (rs180177197, ExAC 0.002%). This variant has been observed in several individuals affected with AGXT-related conditions (PMID: 9604803, 15961946, 27935012, Invitae). ClinVar contains an entry for this variant (Variation ID: 188891). This variant has been reported to affect AGXT protein function (PMID: 24718375, 22018727, 18448374). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 18, 2021

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