ClinVar Miner

Submissions for variant NM_001111125.3(IQSEC2):c.708-3C>T

gnomAD frequency: 0.00002  dbSNP: rs781873807
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000688044 SCV000815641 uncertain significance Intellectual disability, X-linked 1 2023-04-06 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 567855). This variant has been observed in individual(s) with IQSEC2-related conditions (Invitae). This variant is present in population databases (rs781873807, gnomAD 0.005%). This sequence change falls in intron 1 of the IQSEC2 gene. It does not directly change the encoded amino acid sequence of the IQSEC2 protein. It affects a nucleotide within the consensus splice site.
Ambry Genetics RCV002544797 SCV003546271 uncertain significance Inborn genetic diseases 2020-11-04 criteria provided, single submitter clinical testing The c.708-3C>T intronic alteration results from a C to T substitution 3 nucleotides before coding exon 2 of the IQSEC2 gene. Based on data from the Genome Aggregation Database (gnomAD) database, the IQSEC2 c.708-3C>T alteration was observed in 0.00175% (2/114,265) of total alleles studied, with a frequency of 0.0045% (2/44,211) in the European (non-Finnish) subpopulation. This nucleotide position is conserved in available mammalian species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino RCV002227941 SCV002507287 likely pathogenic Tip-toe gait no assertion criteria provided clinical testing

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.