ClinVar Miner

Submissions for variant NM_003482.4(KMT2D):c.15088C>T (p.Arg5030Cys)

dbSNP: rs1555185875
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000513947 SCV000610680 pathogenic not provided 2017-07-19 criteria provided, single submitter clinical testing
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000659821 SCV000781681 uncertain significance Kabuki syndrome 1 2016-11-01 criteria provided, single submitter clinical testing
Clinical Genetics and Genomics, Karolinska University Hospital RCV000513947 SCV001449623 likely pathogenic not provided 2015-11-09 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001857870 SCV002118976 pathogenic Kabuki syndrome 2024-09-23 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 5030 of the KMT2D protein (p.Arg5030Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Kabuki syndrome (PMID: 23320472, 33314698, 35904121). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 445885). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on KMT2D protein function. For these reasons, this variant has been classified as Pathogenic.
MGZ Medical Genetics Center RCV000659821 SCV002580007 likely pathogenic Kabuki syndrome 1 2022-01-13 criteria provided, single submitter clinical testing
GeneDx RCV000513947 SCV003921429 likely pathogenic not provided 2022-10-28 criteria provided, single submitter clinical testing 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: 28475860, 30459467, 27447678, 30107592, 33726816, 23913813, 33314698)

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