ClinVar Miner

Submissions for variant NM_001291415.2(KDM6A):c.1990C>T (p.Arg664Ter)

dbSNP: rs2044403163
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV001265857 SCV001444029 pathogenic Inborn genetic diseases 2019-06-03 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001382692 SCV001581594 pathogenic Kabuki syndrome 2 2024-05-04 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg612*) in the KDM6A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in KDM6A are known to be pathogenic (PMID: 23076834, 23913813). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of Kabuki syndrome (PMID: 29758562). ClinVar contains an entry for this variant (Variation ID: 985115). 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.
GeneDx RCV001546647 SCV001766199 pathogenic not provided 2020-02-11 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 29758562, 25525159, 19330029)
Fulgent Genetics, Fulgent Genetics RCV002504381 SCV002816391 pathogenic Kabuki syndrome 1; Kabuki syndrome 2 2021-12-20 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001382692 SCV005888562 pathogenic Kabuki syndrome 2 2025-03-17 criteria provided, single submitter clinical testing

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