ClinVar Miner

Submissions for variant NM_024757.5(EHMT1):c.1468C>T (p.Arg490Ter)

dbSNP: rs1588553447
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000850475 SCV000992673 likely pathogenic Marfanoid habitus and intellectual disability criteria provided, single submitter research
GeneDx RCV002274105 SCV002559712 pathogenic not provided 2022-07-08 criteria provided, single submitter clinical testing 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; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32277047)
Ambry Genetics RCV003279125 SCV003963124 pathogenic Inborn genetic diseases 2023-04-11 criteria provided, single submitter clinical testing The c.1468C>T (p.R490*) alteration, located in exon 9 (coding exon 9) of the EHMT1 gene, consists of a C to T substitution at nucleotide position 1468. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 490. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been determined to be the result of a de novo mutation in an individual with features consistent with EHMT1-related Kleefstra syndrome (Pan, 2023) and in an individual with intellectual disability and unspecified skeletal features (Chevarin, 2020). Based on the available evidence, this alteration is classified as pathogenic.

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