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NM_022124.6(CDH23):c.5101G>A (p.Glu1701Lys) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 14, 2024
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:
RCV003062274.2

Allele description

NM_022124.6(CDH23):c.5101G>A (p.Glu1701Lys)

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.5101G>A (p.Glu1701Lys)
HGVS:
  • NC_000010.11:g.71778222G>A
  • NG_008835.1:g.386276G>A
  • NM_022124.6:c.5101G>AMANE SELECT
  • NP_071407.4:p.Glu1701Lys
  • NC_000010.10:g.73537979G>A
Protein change:
E1701K
Molecular consequence:
  • NM_022124.6:c.5101G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003441442Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Jan 14, 2024)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Non-syndromic hearing impairment in India: high allelic heterogeneity among mutations in TMPRSS3, TMC1, USHIC, CDH23 and TMIE.

Ganapathy A, Pandey N, Srisailapathy CR, Jalvi R, Malhotra V, Venkatappa M, Chatterjee A, Sharma M, Santhanam R, Chadha S, Ramesh A, Agarwal AK, Rangasayee RR, Anand A.

PLoS One. 2014;9(1):e84773. doi: 10.1371/journal.pone.0084773.

PubMed [citation]
PMID:
24416283
PMCID:
PMC3885616

A novel variant in the CDH23 gene is associated with non-syndromic hearing loss in a Chinese family.

Liang Y, Wang K, Peng Q, Zhu P, Wu C, Rao C, Chang J, Li S, Lu X.

Int J Pediatr Otorhinolaryngol. 2018 Jan;104:108-112. doi: 10.1016/j.ijporl.2017.11.009. Epub 2017 Nov 13.

PubMed [citation]
PMID:
29287849
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003441442.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1701 of the CDH23 protein (p.Glu1701Lys). This variant is present in population databases (rs764025875, gnomAD 0.01%). This missense change has been observed in individuals with deafness (PMID: 24416283, 29287849). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2136884). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CDH23 protein function with a positive predictive value of 80%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Jul 7, 2024