ClinVar Miner

Submissions for variant NM_001384140.1(PCDH15):c.1998-2A>G

dbSNP: rs397517452
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000824733 SCV000063397 pathogenic Rare genetic deafness 2012-04-30 criteria provided, single submitter clinical testing The 1998-2A>G variant (PCDH15) has not been reported in the literature nor previ ously identified by our laboratory. This variant occurs in the invariant region (+/- 1/2) of the splice consensus sequence and is predicted to cause altered spl icing leading to an abnormal or absent protein. In summary, this variant meets our criteria to be classified as pathogenic.
Counsyl RCV000039708 SCV000795879 likely pathogenic Usher syndrome type 1F 2017-11-21 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001379283 SCV001577056 likely pathogenic not provided 2022-02-08 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 16 of the PCDH15 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PCDH15 are known to be pathogenic (PMID: 11398101, 11487575, 14570705). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. ClinVar contains an entry for this variant (Variation ID: 46449). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Baylor Genetics RCV003473288 SCV004200874 pathogenic Autosomal recessive nonsyndromic hearing loss 23 2022-03-22 flagged submission clinical testing

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