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NM_001378609.3(OTOGL):c.6229T>G (p.Cys2077Gly) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jul 26, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV000514672.9

Allele description [Variation Report for NM_001378609.3(OTOGL):c.6229T>G (p.Cys2077Gly)]

NM_001378609.3(OTOGL):c.6229T>G (p.Cys2077Gly)

Gene:
OTOGL:otogelin like [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q21.31
Genomic location:
Preferred name:
NM_001378609.3(OTOGL):c.6229T>G (p.Cys2077Gly)
HGVS:
  • NC_000012.12:g.80358862T>G
  • NG_033008.1:g.154410T>G
  • NM_001368062.3:c.6094T>G
  • NM_001378609.3:c.6229T>GMANE SELECT
  • NM_001378610.3:c.6229T>G
  • NM_173591.7:c.6229T>G
  • NP_001354991.2:p.Cys2032Gly
  • NP_001365538.2:p.Cys2077Gly
  • NP_001365539.2:p.Cys2077Gly
  • NP_775862.3:p.Cys2068Gly
  • NP_775862.4:p.Cys2077Gly
  • NC_000012.11:g.80752642T>G
  • NM_173591.3:c.6202T>G
Protein change:
C2032G
Links:
dbSNP: rs145929269
NCBI 1000 Genomes Browser:
rs145929269
Molecular consequence:
  • NM_001368062.3:c.6094T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378609.3:c.6229T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378610.3:c.6229T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_173591.7:c.6229T>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000609882Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Apr 11, 2017)
germlineclinical testing

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

SCV002538717GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Jul 26, 2023)
germlineclinical testing

Citation Link,

SCV003275572Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jul 17, 2023)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

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 Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000609882.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.000277not providednot provided

From GeneDx, SCV002538717.3

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

Description

Reported without a second variant in unrelated patients with hearing loss in published literature (Roman-Naranjo et al., 2020); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 33136635)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003275572.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024