ClinVar Miner

Submissions for variant NM_025132.4(WDR19):c.2872G>A (p.Ala958Thr)

gnomAD frequency: 0.00003  dbSNP: rs1057523257
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000417853 SCV000531262 uncertain significance not provided 2016-08-31 criteria provided, single submitter clinical testing The A958T variant in the WDR19 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The A958T variant was not observed in approximately 5,900 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The A958T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret A958T as a variant of uncertain significance.
Invitae RCV001861610 SCV002252268 uncertain significance Asphyxiating thoracic dystrophy 5; Senior-Loken syndrome 8 2022-08-10 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 958 of the WDR19 protein (p.Ala958Thr). This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with WDR19-related conditions. ClinVar contains an entry for this variant (Variation ID: 388871). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 RCV002481324 SCV002790345 uncertain significance Asphyxiating thoracic dystrophy 5; Nephronophthisis 13; Cranioectodermal dysplasia 4; Senior-Loken syndrome 8; Spermatogenic failure 72 2021-09-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV002526357 SCV003557028 uncertain significance Inborn genetic diseases 2021-07-06 criteria provided, single submitter clinical testing The c.2872G>A (p.A958T) alteration is located in exon 25 (coding exon 25) of the WDR19 gene. This alteration results from a G to A substitution at nucleotide position 2872, causing the alanine (A) at amino acid position 958 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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