ClinVar Miner

Submissions for variant NM_000440.3(PDE6A):c.1620G>A (p.Glu540=)

gnomAD frequency: 0.00001  dbSNP: rs727504072
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000153659 SCV000203216 uncertain significance not provided 2014-04-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000153659 SCV001211680 likely pathogenic not provided 2024-05-14 criteria provided, single submitter clinical testing This sequence change affects codon 540 of the PDE6A mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PDE6A protein. This variant also falls at the last nucleotide of exon 12, which is part of the consensus splice site for this exon. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with retinitis pigmentosa (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 167432). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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.

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