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NM_012203.2(GRHPR):c.742G>A (p.Val248Ile) AND Primary hyperoxaluria, type II

Germline classification:
Conflicting interpretations of pathogenicity (3 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:
RCV001829926.4

Allele description [Variation Report for NM_012203.2(GRHPR):c.742G>A (p.Val248Ile)]

NM_012203.2(GRHPR):c.742G>A (p.Val248Ile)

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.742G>A (p.Val248Ile)
HGVS:
  • NC_000009.12:g.37432015G>A
  • NG_008135.1:g.14306G>A
  • NM_012203.2:c.742G>AMANE SELECT
  • NP_036335.1:p.Val248Ile
  • NC_000009.11:g.37432012G>A
  • NC_000009.11:g.37432012G>A
  • NM_012203.1:c.742G>A
Protein change:
V248I
Links:
dbSNP: rs369950120
NCBI 1000 Genomes Browser:
rs369950120
Molecular consequence:
  • NM_012203.2:c.742G>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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002075688Natera, Inc.
no assertion criteria provided
Uncertain significance
(Feb 26, 2020)
germlineclinical testing

SCV002790542Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Dec 8, 2021)
unknownclinical testing

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

SCV004174330Clinical Biochemistry Laboratory, Health Services Laboratory
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 27, 2023)
germlinecuration

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedcuration

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., SCV002075688.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002790542.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Clinical Biochemistry Laboratory, Health Services Laboratory, SCV004174330.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

Another mutation (c.743T>A), affecting the same amino acid, has been found in a patient with PH2. ACMG: PM1 PM2 PM5 'Likely pathogenic'

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

Last Updated: Feb 4, 2024