ClinVar Miner

Submissions for variant NM_006618.5(KDM5B):c.1834C>T (p.Arg612Ter)

gnomAD frequency: 0.00002  dbSNP: rs777362026
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn RCV001843855 SCV002103038 uncertain significance not provided 2021-08-11 criteria provided, single submitter clinical testing
GeneDx RCV001843855 SCV003933060 pathogenic not provided 2024-06-24 criteria provided, single submitter clinical testing Reported in individuals with autism in published literature; however, detailed clinical and segregation information was not provided (PMID: 34312540); 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; This variant is associated with the following publications: (PMID: 34312540)
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center RCV004783988 SCV005397781 likely pathogenic Intellectual disability, autosomal recessive 65 2024-06-07 criteria provided, single submitter clinical testing This sequence variant is a single nucleotide substitution (C>T) at position 1834 of the coding sequence of the KDM5B gene that changes the Arg612 codon to an early stop codon. As it occurs in exon 14 of 27, this variant is predicted to generate a non-functional allele through either the expression of a truncated protein or a loss of KDM5B-encoded lysine demethylase 5B expression due to nonsense-mediated decay. This is a previously reported variant (ClinVar 1343255) that has not been observed in the literature in individuals affected by KDM5B-related disorder, to our knowledge. This variant is present in 8 of 1599886 alleles (0.0005%) in the gnomAD v4.1.0 population dataset. Studies examining the functional consequence of this variant have not been published, to our knowledge. Based upon the evidence, we consider this variant to be likely pathogenic. ACMG Criteria: PM2, PVS1

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