ClinVar Miner

Submissions for variant NM_014956.5(CEP164):c.3001C>G (p.Leu1001Val) (rs199637319)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000493085 SCV000582228 uncertain significance not provided 2017-05-08 criteria provided, single submitter clinical testing The L1001V variant in the CEP164 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The L1001V variant is observed in 25/66,380 (0.04%) alleles from individuals of European (non-Finnish) background in the ExAC dataset (Lek et al., 2016). The L1001V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Leucine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret L1001V as a variant of uncertain significance.
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000625376 SCV000745139 uncertain significance Nephronophthisis 15 2016-03-24 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000625376 SCV000896129 uncertain significance Nephronophthisis 15 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000625376 SCV001230056 uncertain significance Nephronophthisis 15 2019-12-04 criteria provided, single submitter clinical testing This sequence change replaces leucine with valine at codon 1001 of the CEP164 protein (p.Leu1001Val). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and valine. This variant is present in population databases (rs199637319, ExAC 0.04%). This variant has not been reported in the literature in individuals with CEP164-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.

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