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NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Jul 14, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000044111.5
Variation ID:
44111
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)

Allele ID
53279
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71706952 (GRCh38) GRCh38 UCSC
10: 73466709 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73466709T>C
NC_000010.11:g.71706952T>C
NG_008835.1:g.315006T>C
... more HGVS
Protein change
-
Other names
p.S1003S:TCT>TCC
Canonical SPDI
NC_000010.11:71706951:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.20747 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.16699
The Genome Aggregation Database (gnomAD), exomes 0.10342
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.13368
The Genome Aggregation Database (gnomAD) 0.15109
Exome Aggregation Consortium (ExAC) 0.14117
The Genome Aggregation Database (gnomAD) 0.13841
Trans-Omics for Precision Medicine (TOPMed) 0.17453
1000 Genomes Project 0.20747
Links
ClinGen: CA133598
dbSNP: rs10823829
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 May 7, 2014 RCV000037087.4
Benign 2 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV000289189.3
Benign 2 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV000341868.3
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001521165.1
Benign 1 no assertion criteria provided Sep 16, 2020 RCV001271856.1
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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
(Dec 28, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000060744.5
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (6)
Comment:
Ser1003Ser in Exon 26A of CDH23: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, … (more)
Benign
(Mar 05, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167605.9
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
(May 07, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228381.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363676.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363675.3
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
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001730449.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750562.1
Submitted: (Jul 14, 2021)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750563.1
Submitted: (Jul 14, 2021)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Natera, Inc.
Accession: SCV001453328.1
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
Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study. Le Quesne Stabej P Journal of medical genetics 2012 PMID: 22135276
Four-year follow-up of diagnostic service in USH1 patients. Roux AF Investigative ophthalmology & visual science 2011 PMID: 21436283
High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays. Kothiyal P BMC biotechnology 2010 PMID: 20146813
Molecular screening of deafness in Algeria: high genetic heterogeneity involving DFNB1 and the Usher loci, DFNB2/USH1B, DFNB12/USH1D and DFNB23/USH1F. Ammar-Khodja F European journal of medical genetics 2009 PMID: 19375528
Survey of the frequency of USH1 gene mutations in a cohort of Usher patients shows the importance of cadherin 23 and protocadherin 15 genes and establishes a detection rate of above 90%. Roux AF Journal of medical genetics 2006 PMID: 16679490
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 - - - -

Text-mined citations for rs10823829...

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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