ClinVar Miner

Submissions for variant NM_181426.2(CCDC39):c.526_527del (p.Leu176fs)

dbSNP: rs780175755
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000168290 SCV000218968 pathogenic Primary ciliary dyskinesia 2024-07-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu176Alafs*10) in the CCDC39 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CCDC39 are known to be pathogenic (PMID: 21131972, 23255504). This variant is present in population databases (rs780175755, gnomAD 0.004%). This premature translational stop signal has been observed in individuals with primary ciliary dyskinesia (PMID: 23255504). ClinVar contains an entry for this variant (Variation ID: 188300). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
3billion RCV003152688 SCV003841720 pathogenic Primary ciliary dyskinesia 14 2023-02-23 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with CCDC39 related disorder (ClinVar ID: VCV000188300 / PMID: 23255504). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
GeneDx RCV004815257 SCV005439253 pathogenic not provided 2024-06-13 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; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31589614, 33577779, 30029678, 32622824, 32367404, 23255504)
Fulgent Genetics, Fulgent Genetics RCV003152688 SCV005661939 pathogenic Primary ciliary dyskinesia 14 2024-02-20 criteria provided, single submitter clinical testing

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