ClinVar Miner

Submissions for variant NM_197968.4(ZMYM2):c.1765C>T (p.Arg589Ter)

dbSNP: rs1952668177
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV001262012 SCV001439377 uncertain significance not provided 2020-09-01 criteria provided, single submitter research ACMG codes:PM2
GeneDx RCV001262012 SCV002549291 likely pathogenic not provided 2022-07-08 criteria provided, single submitter clinical testing Identified in a patient with a neurodevelopmental disorder (Stessman et al., 2017); 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 at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27535533, 33004838, 28191889)
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV002291294 SCV002583826 likely pathogenic Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities 2023-12-01 criteria provided, single submitter clinical testing PVS1_Strong, PS4_Moderate, PM2
Ambry Genetics RCV004967934 SCV005537171 pathogenic Inborn genetic diseases 2024-08-28 criteria provided, single submitter clinical testing The c.1765C>T (p.R589*) alteration, located in exon 10 (coding exon 7) of the ZMYM2 gene, consists of a C to T substitution at nucleotide position 1765. This changes the amino acid from an arginine (R) to a stop codon at amino acid position 589. 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 was reported in an individual with a neurodevelopmental disorder and another individual with unspecified neonatal medical concerns (Stessman, 2017; Bowling, 2022). Based on the available evidence, this alteration is classified as pathogenic.

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