ClinVar Miner

Submissions for variant NM_001039591.3(USP9X):c.1315-4A>G

dbSNP: rs1057522024
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000430135 SCV000525578 pathogenic not provided 2023-03-02 criteria provided, single submitter clinical testing Internal targeted RNA studies in blood from a different male patient referred for testing at GeneDx demonstrate this variant alters RNA splicing by damaging the natural splice acceptor site of intron 10 of the USP9X gene, leading to an aberrant splice product which retains the last three nucleotides of intron 10 between exon 10 and 11 and introduces a premature stop codon predicted to lead to nonsense mediated decay or protein truncation; of note, wild-type transcript was expressed at roughly equal levels indicating a leaky splicing effect; Not observed in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports a deleterious effect on splicing
Baylor Genetics RCV001329531 SCV001520991 likely pathogenic Intellectual disability, X-linked 99 2023-02-01 criteria provided, single submitter clinical testing
Baylor Genetics RCV003333067 SCV004041539 likely pathogenic Intellectual disability, X-linked 99, syndromic, female-restricted 2023-02-01 criteria provided, single submitter clinical testing
GenomeConnect - Brain Gene Registry RCV003984839 SCV004801294 not provided Intellectual disability, X-linked 99; Intellectual disability, X-linked 99, syndromic, female-restricted no assertion provided phenotyping only Variant classified as Likely pathogenic and reported on 02-01-2023 by Baylor Genetics. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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