ClinVar Miner

Submissions for variant NM_017950.4(CCDC40):c.1467C>A (p.Ser489Arg)

dbSNP: rs200154414
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000467464 SCV000547204 uncertain significance Primary ciliary dyskinesia 2023-08-24 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 489 of the CCDC40 protein (p.Ser489Arg). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CCDC40 protein function. ClinVar contains an entry for this variant (Variation ID: 407772). This variant has not been reported in the literature in individuals affected with CCDC40-related conditions. This variant is present in population databases (rs200154414, gnomAD 0.1%).
Ambry Genetics RCV000467464 SCV002698815 uncertain significance Primary ciliary dyskinesia 2018-09-17 criteria provided, single submitter clinical testing The p.S489R variant (also known as c.1467C>A), located in coding exon 10 of the CCDC40 gene, results from a C to A substitution at nucleotide position 1467. The serine at codon 489 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001574020 SCV001800708 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001574020 SCV001967194 likely benign not provided no assertion criteria provided clinical testing

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