NM_138413.4(HOGA1):c.580G>A (p.Gly194Ser) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 14, 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:: RCV003738463.2

Allele description [Variation Report for NM_138413.4(HOGA1):c.580G>A (p.Gly194Ser)]

NM_138413.4(HOGA1):c.580G>A (p.Gly194Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_138413.4(HOGA1):c.580G>A (p.Gly194Ser)

HGVS:

NC_000010.11:g.97599791G>A
NG_027922.1:g.20447G>A
NM_001134670.2:c.212-2066G>A
NM_138413.4:c.580G>AMANE SELECT
NP_612422.2:p.Gly194Ser
NC_000010.10:g.99359548G>A

Protein change:

G194S

Molecular consequence:

NM_001134670.2:c.212-2066G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_138413.4:c.580G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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class I adenylate cyclase [Sedimenticola thiotaurini]
class I adenylate cyclase [Sedimenticola thiotaurini]
gi|821538115|ref|WP_046859995.1|

Protein
hypothetical protein SMc01649 [Sinorhizobium meliloti 1021]
hypothetical protein SMc01649 [Sinorhizobium meliloti 1021]
gi|15966014|ref|NP_386367.1|

Protein
Paraburkholderia sp. WSM4179 Ga0537054_04, whole genome shotgun sequence
Paraburkholderia sp. WSM4179 Ga0537054_04, whole genome shotgun sequence
gi|2498301892|ref|NZ_JARZAF01000000 gnl|WGS:NZ_JARZAF01|Ga0537054_04

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004551268	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Aug 14, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 28711958, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004551268

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Aug 14, 2023)

germline

clinical testing

PubMed (2)
[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

Systematic assessment of urinary hydroxy-oxo-glutarate for diagnosis and follow-up of primary hyperoxaluria type III.

Ventzke A, Feldkötter M, Wei A, Becker J, Beck BB, Hoppe B.

Pediatr Nephrol. 2017 Dec;32(12):2263-2271. doi: 10.1007/s00467-017-3731-3. Epub 2017 Jul 15. Erratum in: Pediatr Nephrol. 2018 Jul;33(7):1275-1276. doi: 10.1007/s00467-018-3944-0.

PubMed [citation]

PMID:: 28711958

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004551268.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 194 of the HOGA1 protein (p.Gly194Ser). This variant is present in population databases (rs763146679, gnomAD 0.0009%). This missense change has been observed in individual(s) with primary hyperoxaluria type III (PMID: 28711958). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HOGA1 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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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