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NM_138413.4(HOGA1):c.860G>T (p.Gly287Val)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Mar 28, 2019)
Last evaluated:
Dec 16, 2018
Accession:
VCV000000030.3
Variation ID:
30
Description:
single nucleotide variant
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NM_138413.4(HOGA1):c.860G>T (p.Gly287Val)

Allele ID
15069
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q24.2
Genomic location
10: 97611535 (GRCh38) GRCh38 UCSC
10: 99371292 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.99371292G>T
NC_000010.11:g.97611535G>T
NM_001134670.1:c.371G>T NP_001128142.1:p.Gly124Val missense
... more HGVS
Protein change
G287V
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00004
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
OMIM: 613597.0002
dbSNP: rs138207257
ClinGen: CA113813
UniProtKB: Q86XE5#VAR_064036
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Dec 16, 2018 RCV000000047.3
Pathogenic 1 criteria provided, single submitter Jul 23, 2018 RCV000798240.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HOGA1 - - GRCh38
GRCh37
109 122

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jan 27, 2017)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type III
Allele origin: unknown
Counsyl
Accession: SCV000789310.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (5)
Pathogenic
(Dec 16, 2018)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type III
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000915488.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (4)
Comment:
The HOGA1 c.860G>T (p.Gly287Val) missense variant was first reported by Belostotsky et al. (2010) in a non-consanguineous Ashkenazi Jewish family with primary hyperoxaluria type 3. ... (more)
Pathogenic
(Jul 23, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000937843.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces glycine with valine at codon 287 of the HOGA1 protein (p.Gly287Val). The glycine residue is highly conserved and there is a ... (more)
Pathogenic
(Sep 10, 2010)
no assertion criteria provided
Method: literature only
HYPEROXALURIA, PRIMARY, TYPE III
Allele origin: germline
OMIM
Accession: SCV000020190.1
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Pathogenic
(Nov 27, 2014)
no assertion criteria provided
Method: in vitro
Primary hyperoxaluria, type III
Allele origin: germline
Clinical Biochemistry Laboratory,Health Services Laboratory
Accession: SCV000239846.1
Submitted: (Nov 27, 2014)
Evidence details
Publications
PubMed (1)
Comment:
Prediction programme. Found in conjunction with c.700+5G>T.

Citations for this variant

Title Author Journal Year Link
HOGA1 Gene Mutations of Primary Hyperoxaluria Type 3 in Tunisian Patients. M'dimegh S Journal of clinical laboratory analysis 2017 PMID: 27561601
4-Hydroxy-2-oxoglutarate aldolase inactivity in primary hyperoxaluria type 3 and glyoxylate reductase inhibition. Riedel TJ Biochimica et biophysica acta 2012 PMID: 22771891
The enzyme 4-hydroxy-2-oxoglutarate aldolase is deficient in primary hyperoxaluria type 3. Williams EL Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2012 PMID: 22391140
Structural and biochemical studies of human 4-hydroxy-2-oxoglutarate aldolase: implications for hydroxyproline metabolism in primary hyperoxaluria. Riedel TJ PloS one 2011 PMID: 21998747
Primary hyperoxaluria type III gene HOGA1 (formerly DHDPSL) as a possible risk factor for idiopathic calcium oxalate urolithiasis. Monico CG Clinical journal of the American Society of Nephrology : CJASN 2011 PMID: 21896830
Mutations in DHDPSL are responsible for primary hyperoxaluria type III. Belostotsky R American journal of human genetics 2010 PMID: 20797690

Record last updated Oct 27, 2019