ClinVar Miner

Submissions for variant NM_001182.5(ALDH7A1):c.394-1G>C

dbSNP: rs1064794053
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000481389 SCV000567683 pathogenic not provided 2022-07-19 criteria provided, single submitter clinical testing Reported in a patient with pyridoxine-dependent epilepsy in the published literature (Coughlin et al., 2019); Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30043187)
Invitae RCV001865441 SCV002308124 likely pathogenic Pyridoxine-dependent epilepsy 2021-05-14 criteria provided, single submitter clinical testing 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, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with ALDH7A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 419701). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 4 of the ALDH7A1 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 ALDH7A1 are known to be pathogenic (PMID: 16491085, 20554659).
Genome-Nilou Lab RCV001865441 SCV004049838 likely pathogenic Pyridoxine-dependent epilepsy 2023-04-11 criteria provided, single submitter clinical testing

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