ClinVar Miner

Submissions for variant NM_022124.6(CDH23):c.5066T>C (p.Met1689Thr) (rs397517334)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000039198 SCV000062882 likely benign not specified 2012-09-22 criteria provided, single submitter clinical testing Met1689Thr in exon 39 of CDH23: This variant is not expected to have clinical si gnificance due to a lack of conservation across species, including mammals. Of note, more than 20 different mammals have a threonine (Thr) at this position des pite high nearby amino acid conservation. In addition, computational analyses ( biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) suggest that the Met1689Thr variant may not impact the protein.
Illumina Clinical Services Laboratory,Illumina RCV000281904 SCV000363775 uncertain significance Deafness, autosomal recessive 12 2018-01-13 criteria provided, single submitter clinical testing 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.
Illumina Clinical Services Laboratory,Illumina RCV000318225 SCV000363776 uncertain significance Usher syndrome type 1D 2018-01-13 criteria provided, single submitter clinical testing 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.
Invitae RCV000912043 SCV001057128 likely benign not provided 2019-12-31 criteria provided, single submitter clinical testing
GenomeConnect, ClinGen RCV000844910 SCV000986717 not provided Deafness, autosomal recessive 12; Usher syndrome type 1D no assertion provided phenotyping only Variant interpretted as Uncertain significance and reported on 01/15/2018 by GTR ID Blueprint Genetics. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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