ClinVar Miner

Submissions for variant NM_006204.4(PDE6C):c.2367+1_2367+5del

dbSNP: rs796051871
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000658573 SCV000780350 likely pathogenic not provided 2017-12-01 criteria provided, single submitter clinical testing
Invitae RCV000658573 SCV002208875 pathogenic not provided 2023-12-01 criteria provided, single submitter clinical testing This sequence change affects a splice site in intron 20 of the PDE6C 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 PDE6C are known to be pathogenic (PMID: 19887631, 23776498, 26103963, 30080950). This variant is present in population databases (rs753310704, gnomAD 0.03%). Disruption of this splice site has been observed in individuals with achromatopsia (PMID: 19615668; Invitae). ClinVar contains an entry for this variant (Variation ID: 8766). 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.
3billion RCV002250457 SCV002521806 pathogenic Cone dystrophy 4 2022-05-22 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%). Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. Two affected offsprings share the same variant (3billion dataset). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (3billion dataset). The variant has been reported to be associated with PDE6C related disorder (ClinVar ID: VCV000008766 / PMID: 19615668). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
OMIM RCV000009311 SCV000029529 pathogenic Achromatopsia 5 2019-03-15 no assertion criteria provided literature only

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