ClinVar Miner

Submissions for variant NM_025216.3(WNT10A):c.487C>T (p.Arg163Trp)

gnomAD frequency: 0.00019  dbSNP: rs368280129
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000522644 SCV000617006 likely pathogenic not provided 2022-10-18 criteria provided, single submitter clinical testing Reported previously in the heterozygous state in individuals with oligodontia with or without other features of ectodermal dysplasia (van den Boogaard et al., 2012; Plaisancie et al., 2013; Ruiz-Heiland et al., 2019); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23401279, 22581971, 24398796, 30426266, 34426522)
Illumina Laboratory Services, Illumina RCV001136663 SCV001296521 benign Tooth agenesis, selective, 4 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Illumina Laboratory Services, Illumina RCV001136664 SCV001296522 uncertain significance SchC6pf-Schulz-Passarge syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina RCV001136665 SCV001296523 uncertain significance Odonto-onycho-dermal dysplasia 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Invitae RCV001239125 SCV001411976 uncertain significance Odonto-onycho-dermal dysplasia; Tooth agenesis, selective, 4 2022-05-15 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 163 of the WNT10A protein (p.Arg163Trp). This variant is present in population databases (rs368280129, gnomAD 0.02%). This missense change has been observed in individuals with clinical features of ectodermal dysplasia (PMID: 22581971, 23401279, 30426266). ClinVar contains an entry for this variant (Variation ID: 189351). 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.
PreventionGenetics, part of Exact Sciences RCV004535152 SCV004117398 uncertain significance WNT10A-related disorder 2023-02-01 criteria provided, single submitter clinical testing The WNT10A c.487C>T variant is predicted to result in the amino acid substitution p.Arg163Trp. This variant has been previously reported in the heterozygous or compound heterozygous state in individuals with isolated hypo/oligodontia and/or tooth agenesis (van den Boogaard et al. 2012. PubMed ID: 22581971; Family 9 in Table 1-Plaisancié et al. 2013. PubMed ID: 23401279; Ruiz-Heiland and Bock. 2019. PubMed ID: 30426266). However, in one study the role of p.Arg163Trp (p.R163W) variant in dental aplasia could not be determined as the variant was not observed in all relatives affected by hypo/oligodontia (Family H, Ruiz-Heiland and Bock. 2019. PubMed ID: 30426266). This variant is reported in 0.015% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-219754816-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Karolinska institutet RCV000172902 SCV000221317 uncertain significance Bladder exstrophy-epispadias-cloacal extrophy complex 2015-03-31 no assertion criteria provided research
Natera, Inc. RCV001136664 SCV002078824 uncertain significance SchC6pf-Schulz-Passarge syndrome 2020-01-22 no assertion criteria provided clinical testing

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