ClinVar Miner

Submissions for variant NM_018418.5(SPATA7):c.1171C>T (p.Arg391Ter)

dbSNP: rs374268850
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000578631 SCV000681383 pathogenic not provided 2020-05-13 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; This variant is associated with the following publications: (PMID: 30054919)
Invitae RCV000678631 SCV001578686 pathogenic Leber congenital amaurosis 3 2023-01-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the SPATA7 protein in which other variant(s) (p.Asn454Lysfs*2) have been determined to be pathogenic (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 489379). This premature translational stop signal has been observed in individual(s) with Leber congenital amaurosis (PMID: 30054919). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg391*) in the SPATA7 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 209 amino acid(s) of the SPATA7 protein.
Genetics and Molecular Pathology, SA Pathology RCV002466542 SCV002761798 pathogenic Retinitis pigmentosa 2020-07-24 criteria provided, single submitter clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000678631 SCV000804719 pathogenic Leber congenital amaurosis 3 2016-09-01 no assertion criteria provided clinical testing

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