NM_138413.4(HOGA1):c.903del (p.Cys302fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 24, 2021
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:: RCV002942118.3

Allele description [Variation Report for NM_138413.4(HOGA1):c.903del (p.Cys302fs)]

NM_138413.4(HOGA1):c.903del (p.Cys302fs)

Gene:

HOGA1:4-hydroxy-2-oxoglutarate aldolase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_138413.4(HOGA1):c.903del (p.Cys302fs)

HGVS:

NC_000010.11:g.97611578del
NG_027922.1:g.32234del
NM_001134670.2:c.414del
NM_138413.4:c.903delMANE SELECT
NP_001128142.1:p.Cys139fs
NP_612422.2:p.Cys302fs
NC_000010.10:g.99371332del
NC_000010.10:g.99371335del

Protein change:

C139fs

Molecular consequence:

NM_001134670.2:c.414del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_138413.4:c.903del - 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
SCV003268967	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 24, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20797690, 22771891, 27096395, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003268967

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 24, 2021)

germline

clinical testing

PubMed (4)
[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

Mutations in DHDPSL are responsible for primary hyperoxaluria type III.

Belostotsky R, Seboun E, Idelson GH, Milliner DS, Becker-Cohen R, Rinat C, Monico CG, Feinstein S, Ben-Shalom E, Magen D, Weissman I, Charon C, Frishberg Y.

Am J Hum Genet. 2010 Sep 10;87(3):392-9. doi: 10.1016/j.ajhg.2010.07.023.

PubMed [citation]

PMID:: 20797690
PMCID:: PMC2933339

4-Hydroxy-2-oxoglutarate aldolase inactivity in primary hyperoxaluria type 3 and glyoxylate reductase inhibition.

Riedel TJ, Knight J, Murray MS, Milliner DS, Holmes RP, Lowther WT.

Biochim Biophys Acta. 2012 Oct;1822(10):1544-52. doi: 10.1016/j.bbadis.2012.06.014. Epub 2012 Jul 5.

PubMed [citation]

PMID:: 22771891
PMCID:: PMC3418427

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003268967.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the HOGA1 protein in which other variant(s) (p.Glu315del) have been determined to be pathogenic (PMID: 20797690, 22771891, 27096395). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with HOGA1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys302Alafs*8) in the HOGA1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 26 amino acid(s) of the HOGA1 protein.

#	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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