NM_000030.3(AGXT):c.346G>A (p.Gly116Arg) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Sep 13, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001236818.2

Allele description [Variation Report for NM_000030.3(AGXT):c.346G>A (p.Gly116Arg)]

NM_000030.3(AGXT):c.346G>A (p.Gly116Arg)

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.346G>A (p.Gly116Arg)
HGVS:
  • NC_000002.12:g.240869350G>A
  • NG_008005.1:g.5606G>A
  • NM_000030.3:c.346G>AMANE SELECT
  • NP_000021.1:p.Gly116Arg
  • NP_000021.1:p.Gly116Arg
  • NP_000021.1:p.Gly116Arg
  • NC_000002.11:g.241808767G>A
  • NM_000030.2:c.346G>A
  • P21549:p.Gly116Arg
Protein change:
G116R
Links:
UniProtKB: P21549#VAR_010971; dbSNP: rs180177207
NCBI 1000 Genomes Browser:
rs180177207
Molecular consequence:
  • NM_000030.3:c.346G>A - 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
SCV001409555Invitaecriteria provided, single submitter
Likely pathogenic
(Sep 13, 2019)
germlineclinical testing

PubMed (5)
[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

Comprehensive mutation screening in 55 probands with type 1 primary hyperoxaluria shows feasibility of a gene-based diagnosis.

Monico CG, Rossetti S, Schwanz HA, Olson JB, Lundquist PA, Dawson DB, Harris PC, Milliner DS.

J Am Soc Nephrol. 2007 Jun;18(6):1905-14. Epub 2007 Apr 25.

PubMed [citation]
PMID:
17460142

Performance evaluation of Sanger sequencing for the diagnosis of primary hyperoxaluria and comparison with targeted next generation sequencing.

Williams EL, Bagg EA, Mueller M, Vandrovcova J, Aitman TJ, Rumsby G.

Mol Genet Genomic Med. 2015 Jan;3(1):69-78. doi: 10.1002/mgg3.118.

PubMed [citation]
PMID:
25629080
PMCID:
PMC4299716
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001409555.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change replaces glycine with arginine at codon 116 of the AGXT protein (p.Gly116Arg). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in several individuals affected with primary hyperoxaluria (PMID: 17460142, 25629080, 10453743, 26252291). ClinVar contains an entry for this variant (Variation ID: 189021). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Sep 18, 2021

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