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NM_022124.6(CDH23):c.8064+1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 28, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001378340.4

Allele description [Variation Report for NM_022124.6(CDH23):c.8064+1G>A]

NM_022124.6(CDH23):c.8064+1G>A

Genes:
LOC111982869:Sharpr-MPRA regulatory region 2121 [Gene]
CDH23:cadherin related 23 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_022124.6(CDH23):c.8064+1G>A
HGVS:
  • NC_000010.11:g.71805998G>A
  • NG_008835.1:g.414052G>A
  • NG_056362.1:g.267G>A
  • NM_001171933.1:c.1344+1G>A
  • NM_001171934.1:c.1344+1G>A
  • NM_022124.6:c.8064+1G>AMANE SELECT
  • NC_000010.10:g.73565755G>A
  • NM_022124.5:c.8064+1G>A
Links:
dbSNP: rs1474524543
NCBI 1000 Genomes Browser:
rs1474524543
Molecular consequence:
  • NM_001171933.1:c.1344+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001171934.1:c.1344+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_022124.6:c.8064+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001575885Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 28, 2023) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Mutation of CDH23, encoding a new member of the cadherin gene family, causes Usher syndrome type 1D.

Bolz H, von Brederlow B, Ramírez A, Bryda EC, Kutsche K, Nothwang HG, Seeliger M, del C-Salcedó Cabrera M, Vila MC, Molina OP, Gal A, Kubisch C.

Nat Genet. 2001 Jan;27(1):108-12.

PubMed [citation]
PMID:
11138009
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001575885.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This sequence change affects a donor splice site in intron 56 of the CDH23 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CDH23 are known to be pathogenic (PMID: 11138009, 21940737). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Usher syndrome (PMID: 35020051). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1067155). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024