NM_012203.2(GRHPR):c.889G>A (p.Ala297Thr) AND Primary hyperoxaluria, type II

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 27, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000666135.3

Allele description [Variation Report for NM_012203.2(GRHPR):c.889G>A (p.Ala297Thr)]

NM_012203.2(GRHPR):c.889G>A (p.Ala297Thr)

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.889G>A (p.Ala297Thr)

HGVS:

NC_000009.12:g.37436684G>A
NG_008135.1:g.18975G>A
NM_012203.2:c.889G>AMANE SELECT
NP_036335.1:p.Ala297Thr
NC_000009.11:g.37436681G>A
NM_012203.1:c.889G>A

Protein change:

A297T

Links:

dbSNP: rs200632069

NCBI 1000 Genomes Browser:

rs200632069

Molecular consequence:

NM_012203.2:c.889G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000790379	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Mar 17, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV004171755	Rare Kidney Stone Consortium and the Mayo Clinic Hyperoxaluria Center, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 27, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25644115, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000790379

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Mar 17, 2017)

unknown

clinical testing

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

Citation Link,

SCV004171755

Rare Kidney Stone Consortium and the Mayo Clinic Hyperoxaluria Center, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 27, 2023)

germline

clinical testing

PubMed (2)
[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	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	clinical testing

Citations

PubMed

Phenotype-Genotype Correlations and Estimated Carrier Frequencies of Primary Hyperoxaluria.

Hopp K, Cogal AG, Bergstralh EJ, Seide BM, Olson JB, Meek AM, Lieske JC, Milliner DS, Harris PC; Rare Kidney Stone Consortium..

J Am Soc Nephrol. 2015 Oct;26(10):2559-70. doi: 10.1681/ASN.2014070698. Epub 2015 Feb 2.

PubMed [citation]

PMID:: 25644115
PMCID:: PMC4587693

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 Counsyl, SCV000790379.1

#	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

From Rare Kidney Stone Consortium and the Mayo Clinic Hyperoxaluria Center, Mayo Clinic, SCV004171755.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

ACMG:PM1 PM2 PM3 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

Last Updated: Feb 4, 2024

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