NM_022124.6(CDH23):c.2568C>G (p.Ile856Met) AND not specified

Clinical significance:Benign (Last evaluated: May 21, 2019)

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:
RCV000603389.2

Allele description [Variation Report for NM_022124.6(CDH23):c.2568C>G (p.Ile856Met)]

NM_022124.6(CDH23):c.2568C>G (p.Ile856Met)

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.2568C>G (p.Ile856Met)
HGVS:
  • NC_000010.11:g.71702192C>G
  • NG_008835.1:g.310246C>G
  • NM_001171930.2:c.2568C>G
  • NM_001171931.2:c.2568C>G
  • NM_022124.6:c.2568C>GMANE SELECT
  • NP_001165401.1:p.Ile856Met
  • NP_001165402.1:p.Ile856Met
  • NP_071407.4:p.Ile856Met
  • NC_000010.10:g.73461949C>G
  • NM_022124.5:c.2568C>G
Protein change:
I856M
Links:
dbSNP: rs188498736
NCBI 1000 Genomes Browser:
rs188498736
Molecular consequence:
  • NM_001171930.2:c.2568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171931.2:c.2568C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022124.6:c.2568C>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

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
SCV000730520GeneDxcriteria provided, single submitter
Benign
(Mar 5, 2018)
germlineclinical testing

Citation Link,

SCV001365639Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(May 21, 2019)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown22not providednot providednot providedclinical testing

Citations

PubMed

Genomic Landscape and Mutational Signatures of Deafness-Associated Genes.

Azaiez H, Booth KT, Ephraim SS, Crone B, Black-Ziegelbein EA, Marini RJ, Shearer AE, Sloan-Heggen CM, Kolbe D, Casavant T, Schnieders MJ, Nishimura C, Braun T, Smith RJH.

Am J Hum Genet. 2018 Oct 4;103(4):484-497. doi: 10.1016/j.ajhg.2018.08.006. Epub 2018 Sep 20.

PubMed [citation]
PMID:
30245029
PMCID:
PMC6174355

Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1.

Yoshimura H, Iwasaki S, Nishio SY, Kumakawa K, Tono T, Kobayashi Y, Sato H, Nagai K, Ishikawa K, Ikezono T, Naito Y, Fukushima K, Oshikawa C, Kimitsuki T, Nakanishi H, Usami S.

PLoS One. 2014;9(3):e90688. doi: 10.1371/journal.pone.0090688.

PubMed [citation]
PMID:
24618850
PMCID:
PMC3949687
See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV000730520.1

#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 Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV001365639.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (3)

Description

The p.Ile856Met variant in CDH23 is classified as benign because it has been identified in 6.3% (1575/24996) of Finnish chromosomes by gnomAD, including a total of 61 homozygous individuals (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not provided2not provided

Last Updated: Jul 7, 2021

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