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NM_022124.6(CDH23):c.3262G>A (p.Val1088Met) AND Usher syndrome type 1D

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Apr 8, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000324074.6

Allele description [Variation Report for NM_022124.6(CDH23):c.3262G>A (p.Val1088Met)]

NM_022124.6(CDH23):c.3262G>A (p.Val1088Met)

Genes:
CDH23:cadherin related 23 [Gene - OMIM - HGNC]
C10orf105:chromosome 10 open reading frame 105 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_022124.6(CDH23):c.3262G>A (p.Val1088Met)
HGVS:
  • NC_000010.11:g.71712706G>A
  • NG_008835.1:g.320760G>A
  • NM_001164375.3:c.*3230C>TMANE SELECT
  • NM_001168390.2:c.*3230C>T
  • NM_001171930.2:c.3262G>A
  • NM_022124.6:c.3262G>AMANE SELECT
  • NP_001165401.1:p.Val1088Met
  • NP_071407.4:p.Val1088Met
  • NC_000010.10:g.73472463G>A
  • NM_022124.5:c.3262G>A
  • c.3262G>A
Protein change:
V1088M
Links:
dbSNP: rs200632520
NCBI 1000 Genomes Browser:
rs200632520
Molecular consequence:
  • NM_001164375.3:c.*3230C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001168390.2:c.*3230C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001171930.2:c.3262G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022124.6:c.3262G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Usher syndrome type 1D (USH1D)
Synonyms:
USHER SYNDROME, TYPE ID
Identifiers:
MONDO: MONDO:0010984; MedGen: C1832845; Orphanet: 231169; Orphanet: 886; OMIM: 601067

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000363693Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Jan 12, 2018) 		germlineclinical testing

Citation Link,

SCV001572160Ocular Genomics Institute, Massachusetts Eye and Ear
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 8, 2021) 		germlineresearch

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000363693.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001572160.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

The CDH23 c.3262G>A variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PM2. Based on this evidence we have classified this variant as Variant of Uncertain Significance.

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

Last Updated: Mar 16, 2024