ClinVar Miner

Submissions for variant NM_015100.4(POGZ):c.2989C>T (p.Arg997Ter)

dbSNP: rs1553212545
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000622483 SCV000741779 pathogenic Inborn genetic diseases 2016-09-13 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV001253002 SCV001428500 likely pathogenic Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome 2018-10-25 criteria provided, single submitter clinical testing
GeneDx RCV002281119 SCV002569825 pathogenic not provided 2022-09-01 criteria provided, single submitter clinical testing Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 414 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (HGMD); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27535533, 24077912, 31782611, 28191890)
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV001253002 SCV002577545 pathogenic Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome 2022-01-18 criteria provided, single submitter clinical testing PVS1, PM2, PP3, PP5
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV001253002 SCV002764835 pathogenic Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome 2021-08-05 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV001253002 SCV004047853 pathogenic Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome criteria provided, single submitter clinical testing The stop gained variant c.2989C>T (p.Arg997Ter) in POGZ gene has been reported previously in heterozygous state in patient affected with White-Sutton syndrome (Assia Batzir et al., 2020). The c.2989C>T variant is novel (not in any individuals) in gnomAD exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic/Likely_pathogenic. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. The nucleotide change c.2989C>T in POGZ is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The observed variant is present in the last exon. For these reasons, this variant has been classified as Pathogenic
Genome-Nilou Lab RCV001253002 SCV004049791 likely pathogenic Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome 2023-04-11 criteria provided, single submitter clinical testing

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