ClinVar Miner

Submissions for variant NM_001242896.3(DEPDC5):c.4733A>G (p.Asp1578Gly)

gnomAD frequency: 0.00009  dbSNP: rs201347461
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000471430 SCV000546506 uncertain significance Familial focal epilepsy with variable foci 2025-01-15 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 1578 of the DEPDC5 protein (p.Asp1578Gly). This variant is present in population databases (rs201347461, gnomAD 0.02%). 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: 407343). 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 RCV001566896 SCV001790484 uncertain significance not provided 2019-06-12 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV002339148 SCV002639116 likely benign Inborn genetic diseases 2023-02-15 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV003418170 SCV004114951 uncertain significance DEPDC5-related disorder 2023-09-28 criteria provided, single submitter clinical testing The DEPDC5 c.4733A>G variant is predicted to result in the amino acid substitution p.Asp1578Gly. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.018% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-32302404-A-G), which is more common than expected for a primary cause of disease. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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