ClinVar Miner

Submissions for variant NM_006929.5(SKIC2):c.2203-1G>A

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV003387668 SCV004099203 likely pathogenic Trichohepatoenteric syndrome 2 2023-07-11 criteria provided, single submitter clinical testing PVS1_Moderate, PM2, PM3
Labcorp Genetics (formerly Invitae), Labcorp RCV003778158 SCV004629330 pathogenic not provided 2024-02-07 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 18 of the SKIV2L 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 SKIV2L are known to be pathogenic (PMID: 22444670). This variant is present in population databases (rs144714933, gnomAD 0.0009%). Disruption of this splice site has been observed in individual(s) with clinical features of SKIV2L-related conditions (PMID: 28496993, 31681265). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 2626980). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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