ClinVar Miner

Submissions for variant NM_001172509.2(SATB2):c.715C>T (p.Arg239Ter) (rs137853127)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000256175 SCV000322291 pathogenic not provided 2018-07-11 criteria provided, single submitter clinical testing The R239X pathogenic variant in the SATB2 gene has been reported previously as a de novo variant in two unrelated individuals with intellectual disability and craniofacial dysmorphisms (Leoyklang et al., 2007; Docker et al., 2014). Functional studies indicate that this variant leads to an abnormal truncated protein that forms a dimer with wild-type SATB2 and interferes with the activity of the wild-type protein suggesting a dominant-negative mechanism (Leoyklang et al., 2007; Leoyklang et al., 2013). The R239X variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret R239X as a pathogenic variant.
Invitae RCV000002627 SCV000835522 pathogenic Chromosome 2q32-q33 deletion syndrome 2019-03-19 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg239*) in the SATB2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported to be de novo in individuals affected with a clinical phenotype including cleft palate, intellectual disability and epilepsy (PMID: 17377962, 24301056). ClinVar contains an entry for this variant (Variation ID: 2519). Loss-of-function variants in SATB2 are known to be pathogenic (PMID: 25885067). For these reasons, this variant has been classified as Pathogenic.
Institute of Human Genetics, University of Leipzig Medical Center RCV000002627 SCV001429212 pathogenic Chromosome 2q32-q33 deletion syndrome 2019-08-20 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Strasbourg University Hospital RCV001257620 SCV001434430 pathogenic Intellectual disability 2020-04-20 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000256175 SCV001447251 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
OMIM RCV000002627 SCV000022785 pathogenic Chromosome 2q32-q33 deletion syndrome 2013-12-04 no assertion criteria provided literature only
GeneReviews RCV000002627 SCV000837665 pathogenic Chromosome 2q32-q33 deletion syndrome 2017-06-02 no assertion criteria provided literature only
Autoinflammatory diseases unit,CHU de Montpellier RCV001261363 SCV001438238 pathogenic Cleft palate 2017-01-23 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000256175 SCV001742494 pathogenic not provided no assertion criteria provided clinical testing

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