ClinVar Miner

Submissions for variant NM_014956.5(CEP164):c.1792G>A (p.Ala598Thr)

gnomAD frequency: 0.00032  dbSNP: rs150956860
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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 RCV001321318 SCV001512143 uncertain significance Nephronophthisis 15 2022-07-12 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 598 of the CEP164 protein (p.Ala598Thr). This variant is present in population databases (rs150956860, gnomAD 0.1%). 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: 1021536). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
Fulgent Genetics, Fulgent Genetics RCV001321318 SCV002776464 uncertain significance Nephronophthisis 15 2022-04-14 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004753282 SCV005356331 uncertain significance CEP164-related disorder 2024-07-22 no assertion criteria provided clinical testing The CEP164 c.1792G>A variant is predicted to result in the amino acid substitution p.Ala598Thr. This variant was reported in an individual with focal segmental glomerulosclerosis (Table S4, Wang et al. 2019. PubMed ID: 31308072). This variant is reported in 0.12% of alleles in individuals of African descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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