ClinVar Miner

Submissions for variant NM_014956.5(CEP164):c.3904C>T (p.Pro1302Ser)

gnomAD frequency: 0.00025  dbSNP: rs201430651
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001229800 SCV001402257 uncertain significance Nephronophthisis 15 2024-12-09 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 1302 of the CEP164 protein (p.Pro1302Ser). This variant is present in population databases (rs201430651, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CEP164-related conditions. ClinVar contains an entry for this variant (Variation ID: 956910). 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 CEP164 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.
Baylor Genetics RCV001229800 SCV001520036 uncertain significance Nephronophthisis 15 2019-08-01 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Ambry Genetics RCV002563731 SCV003646177 uncertain significance Inborn genetic diseases 2022-11-08 criteria provided, single submitter clinical testing The c.3904C>T (p.P1302S) alteration is located in exon 30 (coding exon 28) of the CEP164 gene. This alteration results from a C to T substitution at nucleotide position 3904, causing the proline (P) at amino acid position 1302 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV004778016 SCV005390094 uncertain significance not provided 2024-04-23 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV001229800 SCV005680527 uncertain significance Nephronophthisis 15 2024-05-24 criteria provided, single submitter clinical testing

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