ClinVar Miner

Submissions for variant NM_024757.5(EHMT1):c.2026G>A (p.Gly676Arg)

gnomAD frequency: 0.00001  dbSNP: rs757416132
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital RCV000736114 SCV000864388 benign not specified 2017-10-04 criteria provided, single submitter clinical testing BS1, BS2, BP1, BP4; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, is a missense alteration in a gene for which primarily truncating variants are known to cause disease, and is predicted to be tolerated by multiple functional prediction tools.
Invitae RCV000793881 SCV000933259 benign Kleefstra syndrome 1 2023-10-16 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000736114 SCV002511890 uncertain significance not specified 2022-04-08 criteria provided, single submitter clinical testing Variant summary: EHMT1 c.2026G>A (p.Gly676Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251048 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.2026G>A in individuals affected with Kleefstra Syndrome 1 and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as benign/likely benign, and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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