ClinVar Miner

Submissions for variant NM_014946.3(SPAST):c.1004+3_1004+6del (rs1553315234)

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
Athena Diagnostics Inc RCV000517258 SCV000615374 uncertain significance not specified 2017-06-13 criteria provided, single submitter clinical testing
Invitae RCV000822643 SCV000963453 uncertain significance Spastic paraplegia 4, autosomal dominant 2018-10-10 criteria provided, single submitter clinical testing This sequence change falls in intron 6 of the SPAST gene. It does not directly change the encoded amino acid sequence of the SPAST protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SPAST-related disease. ClinVar contains an entry for this variant (Variation ID: 448437). Nucleotide substitutions within 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 may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. A different variant affecting this nucleotide (c.1004+3A>C) has been determined to be pathogenic (PMID: 28870597). This suggests that this nucleotide is important for normal RNA splicing, and that other variants at this position may also be pathogenic. 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.

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.