ClinVar Miner

Submissions for variant NM_014946.4(SPAST):c.1322-30_1322-2del

dbSNP: rs1553318205
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000518769 SCV000615387 pathogenic not provided 2024-10-24 criteria provided, single submitter clinical testing This variant is expected to severely impact normal RNA splicing, and consequently, protein structure and/or function. This variant has not been reported in large, multi-ethnic general populations. (http://gnomad.broadinstitute.org) This variant has been identified in at least one individual with clinical features associated with this gene.
Labcorp Genetics (formerly Invitae), Labcorp RCV003633512 SCV004548045 uncertain significance Hereditary spastic paraplegia 4 2022-12-12 criteria provided, single submitter clinical testing This sequence change falls in intron 10 of the SPAST gene. It does not directly change the encoded amino acid sequence of the SPAST protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with clinical features of SPAST-related conditions (PMID: 20718791; Invitae). This variant is also known as c.1322-31del29bp (p.I440fs). ClinVar contains an entry for this variant (Variation ID: 448446). 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 may disrupt the consensus splice site. 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.

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