ClinVar Miner

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

dbSNP: rs111514883
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
3billion RCV001808916 SCV002059172 likely benign Koolen-de Vries syndrome 2024-07-30 criteria provided, single submitter clinical testing The variant was observed in gnomAD v4.1.0(allele count: 5, allele frequency 0.0003%), and in individuals without associated symptoms to Koolen-De Vries syndrome(3billion dataset). Therefore, this variant is classified as likely benign according to the recommendation of ACMG/AMP guideline.
Labcorp Genetics (formerly Invitae), Labcorp RCV001808916 SCV003476342 likely pathogenic Koolen-de Vries syndrome 2024-10-22 criteria provided, single submitter clinical testing 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). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with KANSL1-related conditions (internal data). ClinVar contains an entry for this variant (Variation ID: 1333700). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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