ClinVar Miner

Submissions for variant NM_025243.4(SLC19A3):c.1172+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1219632810
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 2
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001268291 SCV001447109 likely pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Invitae RCV003502593 SCV004327466 pathogenic Biotin-responsive basal ganglia disease 2023-06-09 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as 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: 987067). Disruption of this splice site has been observed in individual(s) with clinical features of biotin-responsive basal ganglia disease (PMID: 34276785). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 4 of the SLC19A3 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 SLC19A3 are known to be pathogenic (PMID: 23423671, 23482991).

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.