ClinVar Miner

Submissions for variant NM_001242896.3(DEPDC5):c.4808C>T (p.Pro1603Leu)

gnomAD frequency: 0.00001  dbSNP: rs755174447
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001236788 SCV001409524 uncertain significance Familial focal epilepsy with variable foci 2023-08-27 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1603 of the DEPDC5 protein (p.Pro1603Leu). This variant is present in population databases (rs755174447, gnomAD 0.006%). 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: 962861). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.
GeneDx RCV003320814 SCV004025285 uncertain significance not provided 2023-02-09 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV003448381 SCV004176598 uncertain significance Epilepsy, familial focal, with variable foci 1 2023-03-01 criteria provided, single submitter clinical testing The missense c.4808C>T (p.Pro1603Leu) variant in DEPDC5 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Pro1603Leu variant has allele frequency 0.0004% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Uncertain Significance. The amino acid change p.Pro1603Leu in DEPDC5 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Pro at position 1603 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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