ClinVar Miner

Submissions for variant NM_001291415.2(KDM6A):c.4034+3_4034+6del

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV005199049 SCV005839408 likely pathogenic Kabuki syndrome 2 2024-02-07 criteria provided, single submitter clinical testing This sequence change falls in intron 26 of the KDM6A gene. It does not directly change the encoded amino acid sequence of the KDM6A 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 individual(s) with Kabuki syndrome (PMID: 24527667). In at least one individual the variant was observed to be de novo. 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 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.
GeneDx RCV005199050 SCV005848237 pathogenic not provided 2024-08-14 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 24527667)

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