ClinVar Miner

Submissions for variant NM_025132.4(WDR19):c.3049T>G (p.Phe1017Val)

gnomAD frequency: 0.00001  dbSNP: rs778689889
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001313707 SCV001504211 uncertain significance Asphyxiating thoracic dystrophy 5; Senior-Loken syndrome 8 2021-08-30 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine with valine at codon 1017 of the WDR19 protein (p.Phe1017Val). The phenylalanine residue is highly conserved and there is a small physicochemical difference between phenylalanine and valine. This variant is present in population databases (rs778689889, ExAC 0.003%). This variant has not been reported in the literature in individuals affected with WDR19-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: "Probably Damaging"; Align-GVGD: "Class C15"). 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.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001724291 SCV001950430 uncertain significance Retinitis pigmentosa 2021-04-01 criteria provided, single submitter curation The p.Phe1017Val variant in WDR19 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PM2, PP3. Based on this evidence we have classified this variant as a Variant of Uncertain Significance. If you have any questions about the classification please reach out to the Pierce Lab.
Fulgent Genetics, Fulgent Genetics RCV002486223 SCV002784314 uncertain significance Asphyxiating thoracic dystrophy 5; Nephronophthisis 13; Cranioectodermal dysplasia 4; Senior-Loken syndrome 8; Spermatogenic failure 72 2022-04-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV002543630 SCV003663899 uncertain significance Inborn genetic diseases 2022-11-18 criteria provided, single submitter clinical testing The c.3049T>G (p.F1017V) alteration is located in exon 27 (coding exon 27) of the WDR19 gene. This alteration results from a T to G substitution at nucleotide position 3049, causing the phenylalanine (F) at amino acid position 1017 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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