ClinVar Miner

Submissions for variant NM_018418.5(SPATA7):c.1373del (p.Val458fs)

gnomAD frequency: 0.00002  dbSNP: rs753697847
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000599237 SCV000709917 pathogenic not provided 2019-08-26 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 23847139, 26854980)
Labcorp Genetics (formerly Invitae), Labcorp RCV001860227 SCV002284486 pathogenic Leber congenital amaurosis 3 2023-09-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val458Glufs*48) in the SPATA7 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 142 amino acid(s) of the SPATA7 protein. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the SPATA7 protein. Other variant(s) that disrupt this region (p.Gln465Hisfs*41) have been observed in individuals with SPATA7-related conditions (PMID: 19268277). This suggests that this may be a clinically significant region of the protein. ClinVar contains an entry for this variant (Variation ID: 503686). This premature translational stop signal has been observed in individuals with SPATA7-related conditions (PMID: 26854980; Invitae). This variant is present in population databases (rs753697847, gnomAD 0.006%).
OMIM RCV002264714 SCV002540617 pathogenic Retinitis pigmentosa 94, variable age at onset 2022-06-28 no assertion criteria provided literature only

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