ClinVar Miner

Submissions for variant NM_012330.4(KAT6B):c.5041G>A (p.Glu1681Lys)

dbSNP: rs1564632292
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000681059 SCV000808512 likely pathogenic not provided 2022-12-05 criteria provided, single submitter clinical testing Identified in the de novo state in individuals with developmental disorders, however, detailed clinical information was not provided (Kosmicki et al., 2017; Deciphering Developmental Disorders Study, 2017); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28191890, 32424177, 28135719)
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine RCV003762856 SCV004543848 likely pathogenic Developmental disorder 2023-03-16 criteria provided, single submitter clinical testing
Clinical Genomics Laboratory, Washington University in St. Louis RCV005054242 SCV005688769 uncertain significance KAT6B-related multiple congenital anomalies syndrome 2023-08-29 criteria provided, single submitter clinical testing The KAT6B c.5041G>A (p.Glu1681Lys) variant has been reported in the medical literature. It was observed in one patient reported to have KAT6B-related disorder (Zhang L et al., PMID: 32424177), and observed by the DECIPHER study in a de novo and mosaic state in an individual exhibiting neurodevelopmental phenotypes (but classified in the DECIPHER database as likely benign; Kosmicki J et al., PMID: 28191890). This variant is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. Computational predictors are uncertain/conflicting as to the impact of this variant on KAT6B protein function. This variant has been submitted to ClinVar as likely pathogenic by one laboratory (variation ID: 561698). Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

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