VCV002849904.1 - ClinVar

NM_000274.4(OAT):c.661_701del (p.Gln220_Asp221insTer)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000274.4(OAT):c.661_701del (p.Gln220_Asp221insTer)

Variation ID: 2849904 Accession: VCV002849904.1

Type and length

Deletion, 41 bp

Location

Cytogenetic: 10q26.13 10: 124403868-124403908 (GRCh38) [ NCBI UCSC ] 10: 126092437-126092477 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 20, 2024	Feb 20, 2024	Mar 26, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000274.4:c.661_701del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000265.1:p.Gln220_Asp221insTer	nonsense
NM_001171814.2:c.247_287del	NP_001165285.1:p.Gln82_Asp83insTer	nonsense
NM_001322965.2:c.661_701del	NP_001309894.1:p.Gln220_Asp221insTer	nonsense
NM_001322966.2:c.661_701del	NP_001309895.1:p.Gln220_Asp221insTer	nonsense
NM_001322967.2:c.661_701del	NP_001309896.1:p.Gln220_Asp221insTer	nonsense
NM_001322968.2:c.661_701del	NP_001309897.1:p.Gln220_Asp221insTer	nonsense
NM_001322969.2:c.661_701del	NP_001309898.1:p.Gln220_Asp221insTer	nonsense
NM_001322970.2:c.661_701del	NP_001309899.1:p.Gln220_Asp221insTer	nonsense
NM_001322971.2:c.340_380del	NP_001309900.1:p.Gln113_Asp114insTer	nonsense
NM_001322974.2:c.61_101del	NP_001309903.1:p.Gln20_Asp21insTer	nonsense
NC_000010.11:g.124403869_124403909del
NC_000010.10:g.126092438_126092478del
NG_008861.1:g.20043_20083del
NG_075868.1:g.430_470del
NG_075868.2:g.510_550del
LRG_685:g.20043_20083del
LRG_685t1:c.660_700del41	LRG_685p1:p.Asp221Terfs

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000010.11:124403867:CCCTGAATTGGTTCTACCATGAACGCAGCCACATTTGGATCC:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LOC121815974	-	-	-	GRCh38	-	76
OAT		-	-	GRCh38 GRCh37	588	701

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Ornithine aminotransferase deficiency	Pathogenic (1)	criteria provided, single submitter	Mar 26, 2023	RCV003599737.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Mar 26, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Ornithine aminotransferase deficiency Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004448694.1 First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024	Publications: PubMed (2) PubMed: 1737786‚ 23076989 Comment: For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this … (more) For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with OAT-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp221*) 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). (less)

Comment:

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with OAT-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp221*) 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).

Germline Functional Evidence

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Functional analysis of missense mutations of OAT, causing gyrate atrophy of choroid and retina.	Doimo M	Human mutation	2013	PMID: 23076989
Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.	Brody LC	The Journal of biological chemistry	1992	PMID: 1737786

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_000274.4(OAT):c.661_701del (p.Gln220_Asp221insTer)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...