ClinVar Miner

Submissions for variant NM_003114.5(SPAG1):c.2458A>G (p.Lys820Glu)

gnomAD frequency: 0.00006  dbSNP: rs369552222
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002018498 SCV002303303 uncertain significance Primary ciliary dyskinesia 28 2024-10-14 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 820 of the SPAG1 protein (p.Lys820Glu). This variant is present in population databases (rs369552222, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with SPAG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1513866). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SPAG1 protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV004046784 SCV003883001 uncertain significance Primary ciliary dyskinesia 2023-01-23 criteria provided, single submitter clinical testing The c.2458A>G (p.K820E) alteration is located in exon 18 (coding exon 17) of the SPAG1 gene. This alteration results from a A to G substitution at nucleotide position 2458, causing the lysine (K) at amino acid position 820 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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