ClinVar Miner

Submissions for variant NM_000440.3(PDE6A):c.2302G>T (p.Glu768Ter)

gnomAD frequency: 0.00001  dbSNP: rs759563967
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV001073639 SCV001239190 pathogenic Retinal dystrophy 2019-07-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001381541 SCV001579981 pathogenic not provided 2025-01-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu768*) in the PDE6A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PDE6A are known to be pathogenic (PMID: 7493036, 22128245, 23847139). This variant is present in population databases (rs759563967, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with PDE6A-related conditions. ClinVar contains an entry for this variant (Variation ID: 865985). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001784630 SCV002021645 likely pathogenic Retinitis pigmentosa 43 2021-04-05 criteria provided, single submitter clinical testing
3billion RCV001784630 SCV005904604 pathogenic Retinitis pigmentosa 43 2023-07-24 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.004%). Predicted Consequence/Location: Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic without evidence for the classification (ClinVar ID: VCV000865985 /PMID: 31736247). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

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