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NM_022124.6(CDH23):c.4341T>C (p.Asp1447=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000045945.8
Variation ID:
45945
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.4341T>C (p.Asp1447=)

Allele ID
55110
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71738629 (GRCh38) GRCh38 UCSC
10: 73498386 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73498386T>C
NC_000010.10:g.73498386T>C
NC_000010.11:g.71738629T>C
... more HGVS
Protein change
-
Other names
p.D1447D:GAT>GAC
Canonical SPDI
NC_000010.11:71738628:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.04333 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.01471
1000 Genomes Project 0.04333
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00135
The Genome Aggregation Database (gnomAD) 0.01509
Trans-Omics for Precision Medicine (TOPMed) 0.02141
The Genome Aggregation Database (gnomAD), exomes 0.03744
Trans-Omics for Precision Medicine (TOPMed) 0.02616
Exome Aggregation Consortium (ExAC) 0.03054
Links
ClinGen: CA137426
dbSNP: rs12218564
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Oct 8, 2013 RCV000039179.9
Benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000711152.3
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000285582.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000382311.2
Benign 1 criteria provided, single submitter Aug 25, 2020 RCV001283203.2
Benign 1 no assertion criteria provided Sep 16, 2020 RCV001272896.1
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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, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167612.10
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)
Benign
(Jun 12, 2009)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062863.5
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (3)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363738.3
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
(Aug 25, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156900.2
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001730451.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 31, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000841481.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Oct 08, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000114029.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363737.3
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
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Natera, Inc.
Accession: SCV001455320.1
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
Mutation profile of the CDH23 gene in 56 probands with Usher syndrome type I. Oshima A Human mutation 2008 PMID: 18429043
Distribution and frequencies of CDH23 mutations in Japanese patients with non-syndromic hearing loss. Wagatsuma M Clinical genetics 2007 PMID: 17850630
CDH23 mutation and phenotype heterogeneity: a profile of 107 diverse families with Usher syndrome and nonsyndromic deafness. Astuto LM American journal of human genetics 2002 PMID: 12075507
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CDH23 - - - -
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=10&from=73498386&to=73498386 - - - -

Text-mined citations for rs12218564...

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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 Dec 04, 2021