ClinVar Miner

Submissions for variant NM_025000.4(DCAF17):c.1426T>C (p.Tyr476His)

gnomAD frequency: 0.00039  dbSNP: rs142735693
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000292279 SCV000419279 uncertain significance Woodhouse-Sakati syndrome 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV000292279 SCV002192195 uncertain significance Woodhouse-Sakati syndrome 2022-10-08 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 476 of the DCAF17 protein (p.Tyr476His). This variant is present in population databases (rs142735693, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with DCAF17-related conditions. ClinVar contains an entry for this variant (Variation ID: 332272). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt DCAF17 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.
Ambry Genetics RCV002521332 SCV003658480 uncertain significance Inborn genetic diseases 2020-11-18 criteria provided, single submitter clinical testing The c.1426T>C (p.Y476H) alteration is located in exon 14 (coding exon 14) of the DCAF17 gene. This alteration results from a T to C substitution at nucleotide position 1426, causing the tyrosine (Y) at amino acid position 476 to be replaced by a histidine (H). Based on data from the Genome Aggregation Database (gnomAD) database, the DCAF17 c.1426T>C alteration was observed in 0.03% (81/282588) of total alleles studied, with a frequency of 0.05% (69/128978) in the European (non-Finnish) subpopulation. This amino acid position is well conserved in available vertebrate species. The p.Y476H alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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