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NM_012203.2(GRHPR):c.494G>A (p.Gly165Asp) AND Primary hyperoxaluria

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 26, 2017
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:
RCV000585941.1

Allele description [Variation Report for NM_012203.2(GRHPR):c.494G>A (p.Gly165Asp)]

NM_012203.2(GRHPR):c.494G>A (p.Gly165Asp)

Gene:
GRHPR:glyoxylate and hydroxypyruvate reductase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.2
Genomic location:
Preferred name:
NM_012203.2(GRHPR):c.494G>A (p.Gly165Asp)
HGVS:
  • NC_000009.12:g.37429732G>A
  • NG_008135.1:g.12023G>A
  • NM_012203.2:c.494G>AMANE SELECT
  • NP_036335.1:p.Gly165Asp
  • NC_000009.11:g.37429729G>A
  • NM_012203.1:c.494G>A
Protein change:
G165D
Links:
dbSNP: rs180177314
NCBI 1000 Genomes Browser:
rs180177314
Molecular consequence:
  • NM_012203.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Primary hyperoxaluria
Identifiers:
MONDO: MONDO:0002474; MedGen: C0020501; OMIM: PS259900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000699330Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(May 26, 2017) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699330.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The GRHPR c.494G>A (p.Gly165Asp) variant located in the putative cofactor binding site (Cregeen_2003) involves the alteration of a conserved nucleotide and 4/4 in silico tools (SNPsandGO not captured due to low reliability index) predict a damaging outcome for this variant. Functional studies support these predictions, which the variant significantly decreases glyoxylate reductase activity (Cregeen_2003 and Webster_200). This variant was found in 17/121252 control chromosomes, predominantly observed in the South Asian cohort at a frequency of 0.000969 (16/16508), which does not exceed the estimated maximal expected allele frequency of a pathogenic GRHPR variant (0.0014434). Multiple publications have cited the variant in affected individuals. In addition, a clinical diagnostic laboratory classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

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

Last Updated: Oct 13, 2024