NM_022124.6(CDH23):c.7467C>T (p.Arg2489=) AND not specified

Clinical significance:Benign (Last evaluated: Apr 8, 2013)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000039267.5

Allele description [Variation Report for NM_022124.6(CDH23):c.7467C>T (p.Arg2489=)]

NM_022124.6(CDH23):c.7467C>T (p.Arg2489=)

Gene:
CDH23:cadherin related 23 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_022124.6(CDH23):c.7467C>T (p.Arg2489=)
Other names:
p.R2489R:CGC>CGT
HGVS:
  • NC_000010.11:g.71800740C>T
  • NG_008835.1:g.408794C>T
  • NM_001171932.1:c.*183260C>T
  • NM_001171933.1:c.747C>T
  • NM_001171934.1:c.747C>T
  • NM_022124.6:c.7467C>TMANE SELECT
  • NM_022124.6:c.7467C>TMANE SELECT
  • NP_001165404.1:p.Arg249=
  • NP_001165405.1:p.Arg249=
  • NP_071407.4:p.Arg2489=
  • NP_071407.4:p.Arg2489=
  • NC_000010.10:g.73560497C>T
  • NC_000010.10:g.73560497C>T
  • NM_022124.5:c.7467C>T
  • c.7467C>T
  • p.Arg2489Arg
Links:
dbSNP: rs111033289
NCBI 1000 Genomes Browser:
rs111033289
Molecular consequence:
  • NM_001171932.1:c.*183260C>T - genic downstream transcript variant - [Sequence Ontology: SO:0002152]
  • NM_001171933.1:c.747C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171934.1:c.747C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022124.6:c.7467C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
44

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
SCV000062951Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Sep 12, 2011)
germlineclinical testing

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

SCV000167623GeneDxcriteria provided, single submitter
Benign
(Apr 8, 2013)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided4544not providednot providednot providedclinical testing

Citations

PubMed

Mutation profile of the CDH23 gene in 56 probands with Usher syndrome type I.

Oshima A, Jaijo T, Aller E, Millan JM, Carney C, Usami S, Moller C, Kimberling WJ.

Hum Mutat. 2008 Jun;29(6):E37-46. doi: 10.1002/humu.20761.

PubMed [citation]
PMID:
18429043
PMCID:
PMC2399895

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, Partners HealthCare Personalized Medicine, SCV000062951.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided45not providednot providedclinical testing PubMed (2)

Description

Arg2489Arg in exon 53 of CDH23: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located near a splice junction and is listed is dbSNP (rs111033289) with a frequency of 15% ( 18/120 chromosomes) in the East Asian population and 3.9% (49/1256 chromosomes) in the general population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided45not provided44not provided

From GeneDx, SCV000167623.10

#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

Last Updated: Nov 20, 2021

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