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

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000300416.7
Variation ID:
300416
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.2568C>G (p.Ile856Met)

Allele ID
322005
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71702192 (GRCh38) GRCh38 UCSC
10: 73461949 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73461949C>G
NC_000010.11:g.71702192C>G
NG_008835.1:g.310246C>G
... more HGVS
Protein change
I856M
Other names
-
Canonical SPDI
NC_000010.11:71702191:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00034
The Genome Aggregation Database (gnomAD) 0.00561
1000 Genomes Project 0.00120
Trans-Omics for Precision Medicine (TOPMed) 0.00037
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00032
The Genome Aggregation Database (gnomAD) 0.00921
Links
ClinGen: CA5544251
dbSNP: rs188498736
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts May 21, 2019 RCV000603389.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000352367.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000388322.2
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV000913656.3
Benign 1 no assertion criteria provided Apr 15, 2020 RCV001275942.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CDH23 - - GRCh38
GRCh37
2168 2608

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 05, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000730520.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363653.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363654.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(May 21, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV001365639.1
Submitted: (May 14, 2020)
Evidence details
Publications
PubMed (2)
Comment:
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 … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001058809.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Apr 15, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Natera, Inc.
Accession: SCV001461622.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Genomic Landscape and Mutational Signatures of Deafness-Associated Genes. Azaiez H American journal of human genetics 2018 PMID: 30245029
Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1. Yoshimura H PloS one 2014 PMID: 24618850

Text-mined citations for rs188498736...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021