ClinVar Miner

Submissions for variant NM_015443.4(KANSL1):c.868C>T (p.Arg290Ter)

gnomAD frequency: 0.00006  dbSNP: rs149830411
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000486096 SCV000570441 pathogenic not provided 2022-11-28 criteria provided, single submitter clinical testing Identified in an individual from a developmental delay cohort in the published literature (Wang et al., 2020); 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: 33004838)
Ambry Genetics RCV000623046 SCV000742976 likely pathogenic Inborn genetic diseases 2017-11-17 criteria provided, single submitter clinical testing
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System RCV000678306 SCV000804365 pathogenic Koolen-de Vries syndrome 2018-03-19 criteria provided, single submitter provider interpretation This variant was identified in a 12 year old female with a history of intellectual disability, hypotonia, short stature, atrial septal defect, patent ductus arteriosus, multicystic dysplastic left kidney, congenital valgus foot deformity, constipation, and dysphagia. Dysmorphic facial features include coarse facies, hypertelorism, epicanthal folds, broad nasal tip, and wide spaced teeth. The variant is present in the gnomAD Finnish population at 0.058% but is absent from all other populations with sufficient data. The presence of an inversion polymorphism at 17q21.31 which overlaps KANSL1 complicates the interpretation of this variant. The proband is adopted and parental samples were not available. However, there was very strong clinical correlation between this patient's clinical features and Koolen-DeVries syndrome. In addition, whole exome sequencing identified an additional VUS in a gene of uncertain significance.
Mendelics RCV002248704 SCV002517222 uncertain significance not specified 2022-05-04 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000486096 SCV004042003 likely pathogenic not provided 2023-06-01 criteria provided, single submitter clinical testing KANSL1: PVS1, PS2, BS2
Daryl Scott Lab, Baylor College of Medicine RCV000678306 SCV004102698 pathogenic Koolen-de Vries syndrome 2023-11-10 criteria provided, single submitter clinical testing

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