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NM_138413.4(HOGA1):c.700+5G>T

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: May 26, 2021)
Last evaluated:
Oct 22, 2020
Accession:
VCV000204285.12
Variation ID:
204285
Description:
single nucleotide variant
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NM_138413.4(HOGA1):c.700+5G>T

Allele ID
200671
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q24.2
Genomic location
10: 97600168 (GRCh38) GRCh38 UCSC
10: 99359925 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.99359925G>T
NC_000010.11:g.97600168G>T
NM_138413.4:c.700+5G>T MANE Select
... more HGVS
Protein change
-
Other names
missplicing
Canonical SPDI
NC_000010.11:97600167:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00080
Exome Aggregation Consortium (ExAC) 0.00111
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00215
The Genome Aggregation Database (gnomAD), exomes 0.00124
Trans-Omics for Precision Medicine (TOPMed) 0.00162
1000 Genomes Project 0.00060
Links
ClinGen: CA346911
dbSNP: rs185803104
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 7 criteria provided, multiple submitters, no conflicts Dec 17, 2019 RCV000186492.10
Pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 22, 2020 RCV000520586.5
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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
242 255

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type III
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893163.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Nov 23, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000617211.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.700+5G>T pathogenic variant in the HOGA1 gene has been reported in association with primary hyperoxaluria, and has been proposed as a founder mutation in … (more)
Pathogenic
(Dec 07, 2018)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type III
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000915486.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (6)
Comment:
The HOGA1 c.700+5G>T splice_region variant has been reported in at least six studies in which it is found in at least 36 patients with primary … (more)
Pathogenic
(Apr 05, 2016)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type III
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000711965.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (3)
Comment:
The c.700+5G>T variant in HOGA1 is one of the most common HOGA1 pathogenic varia nts in patients with primary hyperoxaluria type 3 (Belostosky 2010, Williams … (more)
Pathogenic
(Dec 17, 2019)
criteria provided, single submitter
Method: clinical testing
Primary hyperoxaluria, type III
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001194117.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (4)
Comment:
NM_138413.3(HOGA1):c.700+5G>T is classified as pathogenic in the context of primary hyperoxaluria type 3. Sources cited for classification include the following: PMID 22781098, 22391140, 21896830 and … (more)
Pathogenic
(Oct 22, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000931941.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change falls in intron 5 of the HOGA1 gene. It does not directly change the encoded amino acid sequence of the HOGA1 protein, … (more)
Pathogenic
(Apr 23, 2019)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001714359.1
Submitted: (May 26, 2021)
Evidence details
Publications
PubMed (5)
Comment:
PS4, PS3, PP4
Pathogenic
(Nov 27, 2014)
no assertion criteria provided
Method: research
Primary hyperoxaluria, type III
Allele origin: germline
Clinical Biochemistry Laboratory,Health Services Laboratory
Accession: SCV000239854.1
Submitted: (Nov 27, 2014)
Evidence details
Publications
PubMed (3)
Comment:
Abnormally spliced hepatic RNA (PMID:22391140)
Pathogenic
(Jul 09, 2015)
no assertion criteria provided
Method: literature only
Primary hyperoxaluria, type III
Allele origin: germline
GeneReviews
Accession: SCV000246175.1
Submitted: (Jul 31, 2015)
Comment:
Results in an in-frame insertion of 51 bp (17 amino acids).
Evidence details
Publications
PubMed (1)
Other databases
http://www.ncbi.nlm.nih.gov/book…
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Primary hyperoxaluria type III
Allele origin: germline
Natera, Inc.
Accession: SCV001455549.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project. Ceyhan-Birsoy O American journal of human genetics 2019 PMID: 30609409
Cellular degradation of 4-hydroxy-2-oxoglutarate aldolase leads to absolute deficiency in primary hyperoxaluria type 3. MacDonald JR FEBS letters 2016 PMID: 27096395
Primary Hyperoxaluria Type 3 Milliner DS - 2015 PMID: 26401545
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Phenotype-Genotype Correlations and Estimated Carrier Frequencies of Primary Hyperoxaluria. Hopp K Journal of the American Society of Nephrology : JASN 2015 PMID: 25644115
4-hydroxyglutamate is a biomarker for primary hyperoxaluria type 3. Pitt JJ JIMD reports 2015 PMID: 24563386
Novel findings in patients with primary hyperoxaluria type III and implications for advanced molecular testing strategies. Beck BB European journal of human genetics : EJHG 2013 PMID: 22781098
The enzyme 4-hydroxy-2-oxoglutarate aldolase is deficient in primary hyperoxaluria type III. Hoppe B Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2012 PMID: 22851625
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
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
http://www.ncbi.nlm.nih.gov/books/NBK316514/ - - - -

Text-mined citations for rs185803104...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021