ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.5088+2T>C

dbSNP: rs552956642
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001233641 SCV001406245 likely pathogenic not provided 2022-08-16 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 960167). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. This variant is present in population databases (rs552956642, gnomAD 0.02%). This sequence change affects a donor splice site in intron 34 of the SZT2 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 SZT2 are known to be pathogenic (PMID: 23932106, 27248490, 28556953).
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV002510590 SCV002820284 likely pathogenic Developmental and epileptic encephalopathy, 18 criteria provided, single submitter clinical testing The splice donor variant c.4917+2T>C in SZT2 (NM_015284.4) has been submitted to ClinVar as Likely Pathogenic. The variant has not been reported in literature in affected individuals. The c.4917+2T>C variant is observed in 7/30,616 (0.0229%) alleles from individuals of South Asian background in gnomAD Exomes and in 1/978 (0.1022%) alleles from individuals of South Asian background in 1000 Genomes. This variant affects an invariant splice nucleotide and hence is expected to lead to loss of function. Biallelic loss of function variant have been reported before in SZT2 related epileptic encephalopathy. For these reasons, this variant has been classified as Likely Pathogenic.
Genome-Nilou Lab RCV002510590 SCV004174054 likely pathogenic Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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