ClinVar Miner

Submissions for variant NM_001130823.3(DNMT1):c.890A>G (p.Lys297Arg)

gnomAD frequency: 0.00004  dbSNP: rs201025441
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000560910 SCV000651326 uncertain significance Hereditary sensory neuropathy-deafness-dementia syndrome 2024-01-22 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 297 of the DNMT1 protein (p.Lys297Arg). This variant is present in population databases (rs201025441, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with DNMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 472284). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV001722508 SCV000715153 likely benign not provided 2021-04-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV002448767 SCV002677794 likely benign Inborn genetic diseases 2020-12-10 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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