NM_022124.6(CDH23):c.7003del (p.Leu2335fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 1, 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:: RCV001219762.5

Allele description

NM_022124.6(CDH23):c.7003del (p.Leu2335fs)

Gene:

CDH23:cadherin related 23 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_022124.6(CDH23):c.7003del (p.Leu2335fs)

HGVS:

NC_000010.11:g.71798527del
NG_008835.1:g.406581del
NM_001171933.1:c.283del
NM_001171934.1:c.283del
NM_022124.6:c.7003delMANE SELECT
NP_001165404.1:p.Leu95fs
NP_001165405.1:p.Leu95fs
NP_071407.4:p.Leu2335fs
NC_000010.10:g.73558282del
NC_000010.10:g.73558284del
NM_022124.5:c.7003del

Protein change:

L2335fs

Links:

dbSNP: rs1379171478

NCBI 1000 Genomes Browser:

rs1379171478

Molecular consequence:

NM_001171933.1:c.283del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001171934.1:c.283del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022124.6:c.7003del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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AV266902 RIKEN full-length enriched, adult male testis (DH10B) Mus musculus cDNA...
AV266902 RIKEN full-length enriched, adult male testis (DH10B) Mus musculus cDNA clone 4930521G14 3', mRNA sequence
gi|6254939|gnl|dbEST|3375497|dbj|AV 2.1|

Nucleotide
Drosophila melanogaster long non-coding RNA:CR46533 (lncRNA:CR46533), lncRNA
Drosophila melanogaster long non-coding RNA:CR46533 (lncRNA:CR46533), lncRNA
gi|2640079989|ref|NR_190042.1|

Nucleotide
Terapon puta isolate NBFGR:11A1 cytochrome c oxidase subunit I (COX1) gene, part...
Terapon puta isolate NBFGR:11A1 cytochrome c oxidase subunit I (COX1) gene, partial cds; mitochondrial
gi|1904964401|gb|MW008793.1|

Nucleotide
Human chromosome 14 DNA sequence BAC R-102G14 of library RPCI-11 from chromosome...
Human chromosome 14 DNA sequence BAC R-102G14 of library RPCI-11 from chromosome 14 of Homo sapiens (Human), complete sequence
gi|13276119|emb|AL122125.4|

Nucleotide
LOC126859716 [Homo sapiens]
LOC126859716 [Homo sapiens]
Gene ID:126859716

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001391716	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 1, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11138009, 21940737, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001391716

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 1, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Allelic hierarchy of CDH23 mutations causing non-syndromic deafness DFNB12 or Usher syndrome USH1D in compound heterozygotes.

Schultz JM, Bhatti R, Madeo AC, Turriff A, Muskett JA, Zalewski CK, King KA, Ahmed ZM, Riazuddin S, Ahmad N, Hussain Z, Qasim M, Kahn SN, Meltzer MR, Liu XZ, Munisamy M, Ghosh M, Rehm HL, Tsilou ET, Griffith AJ, Zein WM, Brewer CC, et al.

J Med Genet. 2011 Nov;48(11):767-75. doi: 10.1136/jmedgenet-2011-100262. Epub 2011 Sep 22.

PubMed [citation]

PMID:: 21940737

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001391716.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Leu2335Cysfs*38) in the CDH23 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CDH23 are known to be pathogenic (PMID: 11138009, 21940737). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with CDH23-related conditions. ClinVar contains an entry for this variant (Variation ID: 948495). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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