NM_000274.4(OAT):c.697C>T (p.Gln233Ter) AND Ornithine aminotransferase deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 25, 2022
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:: RCV002621041.2

Allele description

NM_000274.4(OAT):c.697C>T (p.Gln233Ter)

Genes:

LOC121815974:Sharpr-MPRA regulatory region 15365 [Gene]
OAT:ornithine aminotransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q26.13

Genomic location:

Preferred name:

NM_000274.4(OAT):c.697C>T (p.Gln233Ter)

HGVS:

NC_000010.11:g.124403872G>A
NG_008861.1:g.20079C>T
NG_075868.1:g.433G>A
NM_000274.4:c.697C>TMANE SELECT
NM_001171814.2:c.283C>T
NM_001322965.2:c.697C>T
NM_001322966.2:c.697C>T
NM_001322967.2:c.697C>T
NM_001322968.2:c.697C>T
NM_001322969.2:c.697C>T
NM_001322970.2:c.697C>T
NM_001322971.2:c.376C>T
NM_001322974.2:c.97C>T
NP_000265.1:p.Gln233Ter
NP_000265.1:p.Gln233Ter
NP_001165285.1:p.Gln95Ter
NP_001309894.1:p.Gln233Ter
NP_001309895.1:p.Gln233Ter
NP_001309896.1:p.Gln233Ter
NP_001309897.1:p.Gln233Ter
NP_001309898.1:p.Gln233Ter
NP_001309899.1:p.Gln233Ter
NP_001309900.1:p.Gln126Ter
NP_001309903.1:p.Gln33Ter
LRG_685t1:c.697C>T
LRG_685:g.20079C>T
LRG_685p1:p.Gln233Ter
NC_000010.10:g.126092441G>A
NM_000274.3:c.697C>T

Protein change:

Q126*

Molecular consequence:

NM_000274.4:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001171814.2:c.283C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322965.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322966.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322967.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322968.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322969.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322970.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322971.2:c.376C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322974.2:c.97C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Ornithine aminotransferase deficiency (GACR)
Synonyms:: OAT deficiency; Ornithine ketoacid aminotransferase deficiency; Gyrate atrophy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009796; MedGen: C0018425; Orphanet: 414; OMIM: 258870

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003510011	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 25, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 1737786, 23076989, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003510011

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 25, 2022)

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

Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.

Brody LC, Mitchell GA, Obie C, Michaud J, Steel G, Fontaine G, Robert MF, Sipila I, Kaiser-Kupfer M, Valle D.

J Biol Chem. 1992 Feb 15;267(5):3302-7.

PubMed [citation]

PMID:: 1737786

Functional analysis of missense mutations of OAT, causing gyrate atrophy of choroid and retina.

Doimo M, Desbats MA, Baldoin MC, Lenzini E, Basso G, Murphy E, Graziano C, Seri M, Burlina A, Sartori G, Trevisson E, Salviati L.

Hum Mutat. 2013 Jan;34(1):229-36. doi: 10.1002/humu.22233. Epub 2012 Oct 17.

PubMed [citation]

PMID:: 23076989

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003510011.2

#	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.Gln233*) in the OAT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OAT are known to be pathogenic (PMID: 1737786, 23076989). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with OAT-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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: Feb 20, 2024

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