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NM_022124.6(CDH23):c.7762G>C (p.Glu2588Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 24, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000046038.7
Variation ID:
46038
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.7762G>C (p.Glu2588Gln)

Allele ID
55203
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71803310 (GRCh38) GRCh38 UCSC
10: 73563067 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73563067G>C
NC_000010.11:g.71803310G>C
NG_008835.1:g.411364G>C
... more HGVS
Protein change
E2588Q, E348Q
Other names
-
Canonical SPDI
NC_000010.11:71803309:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00659 (C)

Allele frequency
1000 Genomes Project 0.00659
Trans-Omics for Precision Medicine (TOPMed) 0.00706
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00819
Exome Aggregation Consortium (ExAC) 0.01439
The Genome Aggregation Database (gnomAD) 0.00577
The Genome Aggregation Database (gnomAD), exomes 0.00907
Links
ClinGen: CA137583
dbSNP: rs41281338
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 Dec 5, 2019 RCV000039274.6
Likely benign 2 criteria provided, multiple submitters, no conflicts May 18, 2021 RCV001104789.2
Benign 2 criteria provided, multiple submitters, no conflicts Dec 6, 2020 RCV001522497.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jul 1, 2021 RCV001104790.2
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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
2136 2571

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001261676.1
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 13, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001261677.1
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, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001475762.1
Submitted: (Dec 30, 2020)
Evidence details
Publications
PubMed (4)
Benign
(Oct 17, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062958.5
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Glu2588Gln in exon 55 of CDH23: This variant is not expected to have clinical si gnificance due to its occurrence at an equal frequency in … (more)
Likely benign
(May 18, 2021)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001653332.1
Submitted: (May 29, 2021)
Evidence details
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001732057.1
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750582.1
Submitted: (Jul 14, 2021)
Evidence details
Benign
(Jun 28, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000714491.1
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 21569298, 20146813, 12075507, 18429043, 11138009)

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
Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis. Bonnet C Orphanet journal of rare diseases 2011 PMID: 21569298
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
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

Text-mined citations for rs41281338...

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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 Sep 26, 2021