ClinVar Miner

Submissions for variant NM_001242896.3(DEPDC5):c.1081+4A>G

dbSNP: rs757563918
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
New York Genome Center RCV001839198 SCV002099142 uncertain significance Epilepsy, familial focal, with variable foci 1 2021-03-02 criteria provided, single submitter clinical testing The c.1081+4A>G splice region variant in intron 15 of 42 of DEPDC5 has not been reported in affected individuals in the available literature. This variant is absent in gnomAD v3 and seen at a very low frequency in gnomaAD v2 (1 heterozygote, allele frequency = 0.000004300) indicating it is not a common benign variant in the populations represented in these databases. In silico predictors suggest this variant might affect splicing (TraP score: 0.893; Splice AI score: Donor Gain 0.38). Given the lack of inheritance data and functional studies supporting its pathogenicity, the c.1081+4A>G variant identified in the DEPDC5 gene is reported as a Variant of Uncertain Significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV003594166 SCV004290873 uncertain significance Familial focal epilepsy with variable foci 2024-08-06 criteria provided, single submitter clinical testing This sequence change falls in intron 15 of the DEPDC5 gene. It does not directly change the encoded amino acid sequence of the DEPDC5 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs757563918, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with DEPDC5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1342447). 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 create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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