ClinVar Miner

Submissions for variant NM_015213.4(DENND5A):c.949+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1849592470
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
3billion, Medical Genetics RCV001808304 SCV002058981 likely pathogenic Developmental and epileptic encephalopathy, 49 2022-01-03 criteria provided, single submitter clinical testing Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_VS).It is not observed in the gnomAD v2.1.1 dataset (PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
Labcorp Genetics (formerly Invitae), Labcorp RCV003698870 SCV004473731 likely pathogenic not provided 2023-05-25 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1333616). This variant has not been reported in the literature in individuals affected with DENND5A-related conditions. This sequence change affects a donor splice site in intron 4 of the DENND5A 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 DENND5A are known to be pathogenic (PMID: 27431290, 27866705).

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