ClinVar Miner

Submissions for variant NM_014516.4(CNOT3):c.563G>A (p.Arg188His)

dbSNP: rs2146595244
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University of Leipzig Medical Center RCV001706786 SCV001934277 likely pathogenic Intellectual developmental disorder with speech delay, autism, and dysmorphic facies 2020-10-28 criteria provided, single submitter clinical testing
Cytogenetique et Genetique Moleculaire, CHU Besancon RCV001706786 SCV005431562 pathogenic Intellectual developmental disorder with speech delay, autism, and dysmorphic facies 2023-08-13 criteria provided, single submitter clinical testing The NM_014516.4:c.563G>A variant is a missense variant in a gene with low rate of benign missense mutations and for which missense mutation is a common mechanism of a disease (Missense Z-score =3,78 ; https://gnomad.broadinstitute.org/) (PP2). This variant was identified in two unrelated probands with global developmental delay and was already reported in two unrelated patients from the literature (PMID: 31201375) (PP5). The variant has been identified as a de novo occurrence, without confirmation of paternity and maternity, in three individual with a phenotype consistent with the gene (PM6). This variant is not present in gnomAD v4.1.0 (PM2; https://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as likely pathogenic for CNOT3-related neurodevelopmental disorders based on the ACMG/AMP criteria applied (PM2 PM6 PP2 PP5).

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