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NM_001292063.2(OTOG):c.1666C>T (p.Gln556Ter) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
May 5, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001090232.25

Allele description [Variation Report for NM_001292063.2(OTOG):c.1666C>T (p.Gln556Ter)]

NM_001292063.2(OTOG):c.1666C>T (p.Gln556Ter)

Gene:
OTOG:otogelin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.1
Genomic location:
Preferred name:
NM_001292063.2(OTOG):c.1666C>T (p.Gln556Ter)
HGVS:
  • NC_000011.10:g.17569177C>T
  • NG_033191.2:g.26805C>T
  • NM_001277269.2:c.1702C>T
  • NM_001292063.2:c.1666C>TMANE SELECT
  • NP_001264198.1:p.Gln568Ter
  • NP_001278992.1:p.Gln556Ter
  • NC_000011.9:g.17590724C>T
  • NC_000011.9:g.17590724C>T
  • NG_033191.1:g.26805C>T
  • NM_001277269.1:c.1702C>T
  • p.Gln568X
Protein change:
Q556*
Links:
dbSNP: rs530874854
NCBI 1000 Genomes Browser:
rs530874854
Molecular consequence:
  • NM_001277269.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001292063.2:c.1666C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001245637CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely pathogenic
(Jan 1, 2020)
germlineclinical testing

Citation Link,

SCV003502184Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(May 5, 2023)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations of the gene encoding otogelin are a cause of autosomal-recessive nonsyndromic moderate hearing impairment.

Schraders M, Ruiz-Palmero L, Kalay E, Oostrik J, del Castillo FJ, Sezgin O, Beynon AJ, Strom TM, Pennings RJ, Zazo Seco C, Oonk AM, Kunst HP, Domínguez-Ruiz M, García-Arumi AM, del Campo M, Villamar M, Hoefsloot LH, Moreno F, Admiraal RJ, del Castillo I, Kremer H.

Am J Hum Genet. 2012 Nov 2;91(5):883-9. doi: 10.1016/j.ajhg.2012.09.012.

PubMed [citation]
PMID:
23122587
PMCID:
PMC3487128

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 CeGaT Center for Human Genetics Tuebingen, SCV001245637.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003502184.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

ClinVar contains an entry for this variant (Variation ID: 870667). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with OTOG-related conditions. This variant is present in population databases (rs530874854, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Gln568*) in the OTOG gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OTOG are known to be pathogenic (PMID: 23122587).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024