ClinVar Miner

Submissions for variant NM_006929.5(SKIC2):c.1404-2A>G

dbSNP: rs1772611373
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department of Paediatrics and Adolescent Medicine, The University of Hong Kong RCV001257082 SCV001364382 likely pathogenic Trichohepatoenteric syndrome 2 2020-06-02 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV003770187 SCV004640778 pathogenic not provided 2023-07-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as 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: 929470). Disruption of this splice site has been observed in individual(s) with trichohepatoenteric syndrome (PMID: 32963807). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 13 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).

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