ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.2038-3C>T

gnomAD frequency: 0.00060  dbSNP: rs578153834
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000476380 SCV000553353 uncertain significance not provided 2022-09-27 criteria provided, single submitter clinical testing This sequence change falls in intron 14 of the SZT2 gene. It does not directly change the encoded amino acid sequence of the SZT2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs578153834, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 411938). 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. 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.
Ambry Genetics RCV002418423 SCV002718756 uncertain significance Inborn genetic diseases 2017-12-18 criteria provided, single submitter clinical testing The c.2038-3C>T intronic variant results from a C to T substitution 3 nucleotides upstream from N/A in the SZT2 gene. This nucleotide position is well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice acceptor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV003446066 SCV004174043 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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