ClinVar Miner

Submissions for variant NM_000096.4(CP):c.2065C>T (p.Pro689Ser)

gnomAD frequency: 0.00001  dbSNP: rs200353789
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002040280 SCV002300314 uncertain significance Deficiency of ferroxidase 2023-10-13 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 689 of the CP protein (p.Pro689Ser). This variant is present in population databases (rs200353789, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with CP-related conditions. ClinVar contains an entry for this variant (Variation ID: 1507918). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CP protein function. 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 RCV003348755 SCV004066973 uncertain significance Inborn genetic diseases 2023-09-13 criteria provided, single submitter clinical testing The c.2065C>T (p.P689S) alteration is located in exon 11 (coding exon 11) of the CP gene. This alteration results from a C to T substitution at nucleotide position 2065, causing the proline (P) at amino acid position 689 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV004774610 SCV005385290 uncertain significance not provided 2024-01-08 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Also known as P670S

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