NM_012203.2(GRHPR):c.494G>A (p.Gly165Asp) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 31, 2024
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:: RCV000802868.7

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000942714	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 31, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 24116921, 25629080, 31685312, 11030416, 14635115, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000942714

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 31, 2024)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Ethnic differences in GRHPR mutations in patients with primary hyperoxaluria type 2.

Takayama T, Takaoka N, Nagata M, Johnin K, Okada Y, Tanaka S, Kawamura M, Inokuchi T, Ohse M, Kuhara T, Tanioka F, Yamada H, Sugimura H, Ozono S.

Clin Genet. 2014 Oct;86(4):342-8. doi: 10.1111/cge.12292. Epub 2013 Nov 5.

PubMed [citation]

PMID:: 24116921

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 (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000942714.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 165 of the GRHPR protein (p.Gly165Asp). This variant is present in population databases (rs180177314, gnomAD 0.08%). This missense change has been observed in individual(s) with primary hyperoxaluria type 2 (PMID: 24116921, 25629080, 31685312). ClinVar contains an entry for this variant (Variation ID: 204235). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects GRHPR function (PMID: 11030416, 14635115). For these reasons, this variant has been classified as Pathogenic.

#	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: Oct 13, 2024

ClinVar

Relating variation to medicine