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NM_001292063.2(OTOG):c.2464C>T (p.Gln822Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Nov 19, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000417941.16
Variation ID:
417941
Description:
single nucleotide variant
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NM_001292063.2(OTOG):c.2464C>T (p.Gln822Ter)

Allele ID
404799
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.1
Genomic location
11: 17574890 (GRCh38) GRCh38 UCSC
11: 17596437 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.9:g.17596437C>T
NM_001277269.1:c.2500C>T NP_001264198.1:p.Gln834Ter nonsense
NC_000011.10:g.17574890C>T
... more HGVS
Protein change
Q834*, Q822*
Other names
-
Canonical SPDI
NC_000011.10:17574889:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00061
Trans-Omics for Precision Medicine (TOPMed) 0.00035
The Genome Aggregation Database (gnomAD) 0.00040
Exome Aggregation Consortium (ExAC) 0.00076
The Genome Aggregation Database (gnomAD), exomes 0.00038
Trans-Omics for Precision Medicine (TOPMed) 0.00038
Links
ClinGen: CA5905625
dbSNP: rs554847663
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Jul 22, 2021 RCV000477813.4
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts May 18, 2021 RCV000578779.6
Pathogenic 1 criteria provided, single submitter Apr 14, 2020 RCV000616086.3
Likely pathogenic 1 criteria provided, single submitter Feb 7, 2019 RCV001007897.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
OTOG - - GRCh38
GRCh37
684 707

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 18b
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893872.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Likely pathogenic
(Feb 07, 2019)
criteria provided, single submitter
Method: clinical testing
Intellectual disability
Seizures
(Autosomal recessive inheritance)
Allele origin: maternal
Genomic Medicine Lab, University of California San Francisco
Study: CSER
Accession: SCV001167603.1
Submitted: (Sep 17, 2019)
Evidence details
Pathogenic
(Dec 21, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001206868.1
Submitted: (Feb 06, 2020)
Evidence details
Comment:
This sequence change creates a premature translational stop signal (p.Gln834*) in the OTOG gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Apr 14, 2020)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000712161.3
Submitted: (Jun 03, 2020)
Evidence details
Publications
PubMed (2)
Comment:
The p.Gln834X variant in OTOG has been identified in 4 individuals with hearing loss: 2 heterozygotes where a second variant was not identified on the … (more)
Pathogenic
(Jul 22, 2021)
criteria provided, single submitter
Method: research
Deafness, autosomal recessive 18b
Allele origin: maternal
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: AGHI WGS
Accession: SCV001870382.1
Submitted: (Sep 09, 2021)
Evidence details
Comment:
ACMG codes:PVS1, PM2, PP5
Pathogenic
(May 18, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000680934.2
Submitted: (Sep 30, 2021)
Evidence details
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This … (more)
Likely pathogenic
(May 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000891954.8
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(Jul 19, 2016)
no assertion criteria provided
Method: research
Deafness, autosomal recessive 18b
Allele origin: germline
Division of Human Genetics,Children's Hospital of Philadelphia
Study: CSER-PediSeq
Accession: SCV000536895.1
Submitted: (Jan 23, 2017)
Evidence details
Pathogenic
(Nov 30, 2019)
no assertion criteria provided
Method: clinical testing
Deafness, autosomal recessive 18b
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002020598.1
Submitted: (Nov 19, 2021)
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
Utility and limitations of exome sequencing as a genetic diagnostic tool for children with hearing loss. Sheppard S Genetics in medicine : official journal of the American College of Medical Genetics 2018 PMID: 29907799
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
Targeted disruption of otog results in deafness and severe imbalance. Simmler MC Nature genetics 2000 PMID: 10655058

Text-mined citations for rs554847663...

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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 Nov 28, 2021