ClinVar Miner

Submissions for variant NM_003114.5(SPAG1):c.897_901del (p.Lys301fs)

gnomAD frequency: 0.00009  dbSNP: rs751845138
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000515010 SCV000610411 pathogenic not provided 2017-06-14 criteria provided, single submitter clinical testing
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV001270130 SCV001449000 likely pathogenic Primary ciliary dyskinesia 28 2018-06-04 criteria provided, single submitter clinical testing
GeneDx RCV000515010 SCV001776547 pathogenic not provided 2024-02-23 criteria provided, single submitter clinical testing Frameshift 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: 30293640)
Fulgent Genetics, Fulgent Genetics RCV001270130 SCV002779743 likely pathogenic Primary ciliary dyskinesia 28 2022-04-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001270130 SCV003440549 pathogenic Primary ciliary dyskinesia 28 2023-04-01 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 445743). This premature translational stop signal has been observed in individual(s) with primary ciliary dyskinesia (PMID: 24055112). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs751845138, gnomAD 0.005%). This sequence change creates a premature translational stop signal (p.Lys301Thrfs*4) in the SPAG1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPAG1 are known to be pathogenic (PMID: 24055112).

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