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NM_001292063.2(OTOG):c.8364G>C (p.Leu2788=) AND not specified

Germline classification:
Benign (4 submissions)
Last evaluated:
May 9, 2017
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:
RCV000213413.9

Allele description [Variation Report for NM_001292063.2(OTOG):c.8364G>C (p.Leu2788=)]

NM_001292063.2(OTOG):c.8364G>C (p.Leu2788=)

Gene:
OTOG:otogelin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.1
Genomic location:
Preferred name:
NM_001292063.2(OTOG):c.8364G>C (p.Leu2788=)
HGVS:
  • NC_000011.10:g.17642195G>C
  • NG_033191.2:g.99823G>C
  • NM_001277269.2:c.8400G>C
  • NM_001292063.2:c.8364G>CMANE SELECT
  • NP_001264198.1:p.Leu2800=
  • NP_001264198.1:p.Leu2800=
  • NP_001278992.1:p.Leu2788=
  • NC_000011.9:g.17663742G>C
  • NM_001277269.1:c.8400G>C
  • p.Leu2800Leu
Links:
dbSNP: rs2023483
NCBI 1000 Genomes Browser:
rs2023483
Molecular consequence:
  • NM_001277269.2:c.8400G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001292063.2:c.8364G>C - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
502

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000269533Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Benign
(Nov 24, 2014)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000717097GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(May 9, 2017)
germlineclinical testing

Citation Link,

SCV001741275Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Benigngermlineclinical testing

SCV001956240Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided512502not providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269533.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided512not providednot providedclinical testing PubMed (1)

Description

Leu2800Leu in exon 52 of OTOG: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 58.8% (114/194) of Luhya (Kenyan) chromosomes from a broad population by the 1000 Genomes Project ( http://www.ncbi.nlm.nih.gov/projects/SNP; dbSNP rs2023483).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided512not provided502not provided

From GeneDx, SCV000717097.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001741275.3

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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001956240.1

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

Last Updated: Feb 28, 2024