ClinVar Miner

Submissions for variant NM_001353921.2(ARHGEF9):c.886C>T (p.Arg296Ter)

dbSNP: rs1135401795
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris RCV000496205 SCV000586750 pathogenic Developmental and epileptic encephalopathy, 8 2017-01-06 criteria provided, single submitter clinical testing Intellectual Disability; relative macrocephaly
GeneDx RCV000627195 SCV000748179 pathogenic not provided 2023-02-13 criteria provided, single submitter clinical testing 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 in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26633542, 31440721, 34851771, 33600053, 28708303)
Invitae RCV000496205 SCV000823964 pathogenic Developmental and epileptic encephalopathy, 8 2022-06-09 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This sequence change creates a premature translational stop signal (p.Arg289*) in the ARHGEF9 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ARHGEF9 are known to be pathogenic (PMID: 25678704, 26834553, 28589176). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with early infantile epileptic encephalopathy (PMID: 28708303). ClinVar contains an entry for this variant (Variation ID: 431121). For these reasons, this variant has been classified as Pathogenic.
Genomic Medicine Lab, University of California San Francisco RCV002286412 SCV002576343 pathogenic Global developmental delay criteria provided, single submitter clinical testing
Revvity Omics, Revvity Omics RCV000496205 SCV003815600 pathogenic Developmental and epileptic encephalopathy, 8 2022-05-18 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000627195 SCV003917798 pathogenic not provided 2023-01-01 criteria provided, single submitter clinical testing ARHGEF9: PVS1, PS2, PM2

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