ClinVar Miner

Submissions for variant NM_015443.4(KANSL1):c.2542-1G>A

dbSNP: rs111514883
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
3billion RCV001808916 SCV002059172 likely benign Koolen-de Vries syndrome 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 It is not observed in the gnomAD v2.1.1 dataset . However, The variant has been observed in unaffected individuals in 3billion dataset. Therefore, this variant is classified as likely benign according to the recommendation of ACMG/AMP guideline.
Invitae RCV001808916 SCV003476342 likely pathogenic Koolen-de Vries syndrome 2023-04-10 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. ClinVar contains an entry for this variant (Variation ID: 1333700). Disruption of this splice site has been observed in individual(s) with KANSL1-related conditions (Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 10 of the KANSL1 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 KANSL1 are known to be pathogenic (PMID: 22544363, 22544367).

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.