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NM_022124.6(CDH23):c.7630T>C (p.Leu2544=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000046036.9
Variation ID:
46036
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.7630T>C (p.Leu2544=)

Allele ID
55201
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71803045 (GRCh38) GRCh38 UCSC
10: 73562802 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73562802T>C
NC_000010.11:g.71803045T>C
NG_008835.1:g.411099T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:71803044:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00739 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00370
Trans-Omics for Precision Medicine (TOPMed) 0.00938
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00967
The Genome Aggregation Database (gnomAD) 0.01000
1000 Genomes Project 0.00739
Trans-Omics for Precision Medicine (TOPMed) 0.00934
Exome Aggregation Consortium (ExAC) 0.00437
The Genome Aggregation Database (gnomAD) 0.00947
Links
ClinGen: CA137579
dbSNP: rs114819374
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 5 criteria provided, multiple submitters, no conflicts Dec 6, 2020 RCV000515005.8
Benign 1 criteria provided, single submitter Feb 8, 2012 RCV000039272.2
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001102865.1
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001102866.1
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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 06, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001119968.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Feb 08, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062956.5
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (2)
Comment:
Leu2544Leu in exon 54 of CDH23: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more)
Likely benign
(Apr 11, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000609731.1
Submitted: (Oct 05, 2017)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001259557.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001259558.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001881656.1
Submitted: (Sep 16, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001922104.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001968133.1
Submitted: (Sep 21, 2021)
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
High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays. Kothiyal P BMC biotechnology 2010 PMID: 20146813
Mutation profile of the CDH23 gene in 56 probands with Usher syndrome type I. Oshima A Human mutation 2008 PMID: 18429043

Text-mined citations for rs114819374...

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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