NM_022124.6(CDH23):c.9015G>A (p.Ala3005=) AND not specified

Clinical significance:Benign (Last evaluated: Apr 18, 2014)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000039301.6

Allele description [Variation Report for NM_022124.6(CDH23):c.9015G>A (p.Ala3005=)]

NM_022124.6(CDH23):c.9015G>A (p.Ala3005=)

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.9015G>A (p.Ala3005=)
Other names:
p.A3005A:GCG>GCA
HGVS:
  • NC_000010.11:g.71810507G>A
  • NG_008835.1:g.418561G>A
  • NM_001171933.1:c.2295G>A
  • NM_001171934.1:c.2295G>A
  • NM_022124.6:c.9015G>AMANE SELECT
  • NM_022124.6:c.9015G>AMANE SELECT
  • NP_001165404.1:p.Ala765=
  • NP_001165405.1:p.Ala765=
  • NP_071407.4:p.Ala3005=
  • NP_071407.4:p.Ala3005=
  • NC_000010.10:g.73570264G>A
  • NC_000010.10:g.73570264G>A
  • NM_001171932.1:c.*193027G>A
  • NM_022124.5:c.9015G>A
  • NP_071407.4:p.(=)
  • c.9015G>A
  • p.Ala3005Ala
Links:
dbSNP: rs376497158
NCBI 1000 Genomes Browser:
rs376497158
Molecular consequence:
  • NM_001171933.1:c.2295G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171934.1:c.2295G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022124.6:c.9015G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
18

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000062985Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Apr 30, 2012)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV000167627GeneDxcriteria provided, single submitter
Benign
(Apr 18, 2014)
germlineclinical testing

Citation Link,

SCV000202386EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Apr 16, 2014)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided1818not providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

CDH23 mutation and phenotype heterogeneity: a profile of 107 diverse families with Usher syndrome and nonsyndromic deafness.

Astuto LM, Bork JM, Weston MD, Askew JW, Fields RR, Orten DJ, Ohliger SJ, Riazuddin S, Morell RJ, Khan S, Riazuddin S, Kremer H, van Hauwe P, Moller CG, Cremers CW, Ayuso C, Heckenlively JR, Rohrschneider K, Spandau U, Greenberg J, Ramesar R, Reardon W, et al.

Am J Hum Genet. 2002 Aug;71(2):262-75. Epub 2002 Jun 19.

PubMed [citation]
PMID:
12075507
PMCID:
PMC379159

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000062985.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided18not providednot providedclinical testing PubMed (2)

Description

Ala3005Ala in exon 62 of CDH23: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located near a splice junction, has been identified in 0.4% (30/6796) of European American ch romosomes from a broad population by the NHLBI Exome sequencing project (http:// evs.gs.washington.edu/EVS/; dbSNP rs41304884), and is reported as benign in one publication (Astuto 2002).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided18not provided18not provided

From GeneDx, SCV000167627.10

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000202386.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Dec 4, 2021

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