NM_012203.2(GRHPR):c.593_594del (p.Glu198fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 17, 2023
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:: RCV000799744.5

Allele description [Variation Report for NM_012203.2(GRHPR):c.593_594del (p.Glu198fs)]

NM_012203.2(GRHPR):c.593_594del (p.Glu198fs)

Gene:

GRHPR:glyoxylate and hydroxypyruvate reductase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9p13.2

Genomic location:

Preferred name:

NM_012203.2(GRHPR):c.593_594del (p.Glu198fs)

HGVS:

NC_000009.11:g.37429826_37429827del
NC_000009.12:g.37429829AG[1]
NG_008135.1:g.12120AG[1]
NM_012203.2:c.593_594delMANE SELECT
NP_036335.1:p.Glu198fs
NC_000009.11:g.37429826AG[1]
NC_000009.11:g.37429826_37429827del
NC_000009.11:g.37429826_37429827delAG
NM_012203.1:c.593_594delAG

Protein change:

E198fs

Links:

dbSNP: rs1588757756

NCBI 1000 Genomes Browser:

rs1588757756

Molecular consequence:

NM_012203.2:c.593_594del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000939420	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25644115, 31980526, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000939420

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 17, 2023)

germline

clinical testing

PubMed (3)
[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

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

Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging.

Hou YC, Yu HC, Martin R, Cirulli ET, Schenker-Ahmed NM, Hicks M, Cohen IV, Jönsson TJ, Heister R, Napier L, Swisher CL, Dominguez S, Tang H, Li W, Perkins BA, Barea J, Rybak C, Smith E, Duchicela K, Doney M, Brar P, Hernandez N, et al.

Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):3053-3062. doi: 10.1073/pnas.1909378117. Epub 2020 Jan 24.

PubMed [citation]

PMID:: 31980526
PMCID:: PMC7022190

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000939420.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Glu198Valfs*6) in the GRHPR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GRHPR are known to be pathogenic (PMID: 25644115). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with hyperoxaluria (PMID: 31980526). ClinVar contains an entry for this variant (Variation ID: 645622). 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: Sep 29, 2024

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