ClinVar Miner

Submissions for variant NM_021222.3(PRUNE1):c.316G>A (p.Asp106Asn) (rs773618224)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine RCV000454333 SCV000537906 likely pathogenic Abnormality of brain morphology criteria provided, single submitter research There are 3 more families with similar phenotype
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000490535 SCV000966201 pathogenic Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies 2018-05-09 criteria provided, single submitter clinical testing Observed as a homozygote.
CeGaT Praxis fuer Humangenetik Tuebingen RCV001090402 SCV001245938 pathogenic not provided 2018-05-01 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000490535 SCV001251444 pathogenic Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies 2019-10-29 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000490535 SCV001251858 pathogenic Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies 2020-05-03 criteria provided, single submitter clinical testing
Invitae RCV001090402 SCV001576800 likely pathogenic not provided 2017-10-18 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid with asparagine at codon 106 of the PRUNE1 protein (p.Asp106Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine. This variant is present in population databases (rs773618224, ExAC 0.02%). This variant has been reported to be homozygous in several individuals with syndromic intellectual disability (PMID: 26539891, 28334956). ClinVar contains an entry for this variant (Variation ID: 402131). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001090402 SCV001762256 pathogenic not provided 2021-06-17 criteria provided, single submitter clinical testing
OMIM RCV000490535 SCV000577901 pathogenic Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies 2017-09-19 no assertion criteria provided literature only
Institute of Human Genetics, Klinikum rechts der Isar RCV000490535 SCV000680349 pathogenic Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies 2020-01-16 no assertion criteria provided clinical testing

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