NM_012203.2(GRHPR):c.139C>T (p.Arg47Ter) AND Primary hyperoxaluria, type II

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Oct 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000779582.9

Allele description [Variation Report for NM_012203.2(GRHPR):c.139C>T (p.Arg47Ter)]

NM_012203.2(GRHPR):c.139C>T (p.Arg47Ter)

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.139C>T (p.Arg47Ter)

HGVS:

NC_000009.12:g.37424900C>T
NG_008135.1:g.7191C>T
NM_012203.2:c.139C>TMANE SELECT
NP_036335.1:p.Arg47Ter
NC_000009.11:g.37424897C>T
NM_012203.1:c.139C>T

Protein change:

R47*

Links:

dbSNP: rs774654020

NCBI 1000 Genomes Browser:

rs774654020

Molecular consequence:

NM_012203.2:c.139C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Primary hyperoxaluria, type II (HP2)
Synonyms:: OXALOSIS II; Primary hyperoxaluria type 2; Oxalosis 2; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009824; MedGen: C0268165; Orphanet: 416; Orphanet: 93599; OMIM: 260000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001458445	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV004174336	Clinical Biochemistry Laboratory, Health Services Laboratory	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 27, 2023)	germline	curation	PubMed (1) [See all records that cite this PMID]
SCV004191702	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 26, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001458445

Natera, Inc.

no assertion criteria provided

Pathogenic
(Sep 16, 2020)

germline

clinical testing

SCV004174336

Clinical Biochemistry Laboratory, Health Services Laboratory

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 27, 2023)

germline

curation

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

SCV004191702

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 26, 2023)

unknown

clinical testing

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

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

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 Natera, Inc., SCV001458445.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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

From Clinical Biochemistry Laboratory, Health Services Laboratory, SCV004174336.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

Description

ACMG:PVS1 PM2 PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004191702.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 23, 2024

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