ClinVar Miner

Submissions for variant NM_001399.5(EDA):c.612_629del (p.202_204IPG[1]) (rs1064793104)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000487168 SCV000564954 likely pathogenic not provided 2016-03-09 criteria provided, single submitter clinical testing The c.612_629del18 variant in the EDA1 gene is an in-frame deletion that results in the loss of residues Isoleucine 205 through Glycine 210. The c.612_629del18 variant has been reported (as c.612-619del) as a hemizygous variant in a child diagnosed with non-syndromic tooth agenesis (Arte et al., 2013). The variant was also reported to have arisen de novo (Arte et al., 2013). The c.612_629del18 variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This deletion results in the loss of two residues that are conserved in mammals and four residues that are conserved conserved across species. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Invitae RCV000805136 SCV000945081 pathogenic Hypohidrotic X-linked ectodermal dysplasia 2019-09-24 criteria provided, single submitter clinical testing This variant, c.612_629del, results in the deletion of 6 amino acid(s) of the EDA protein (p.Ile205_Gly210del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed to be hemizygous in an individual with clinical features of ectodermal dysplasia (Invitae) and was observed to be de novo in an individual affected with non-syndromic tooth agenesis (PMID: 23991204). ClinVar contains an entry for this variant (Variation ID: 418170). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant disrupts the p.Pro206 amino acid residue in EDA. Other variant(s) that disrupt this residue have been observed in individuals with EDA-related conditions (Invitae), suggesting that it is a clinically significant residue. As a result, variants that disrupt this residue are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.
Molecular Diagnostics Laboratory, M Health: University of Minnesota RCV000805136 SCV001142706 likely pathogenic Hypohidrotic X-linked ectodermal dysplasia 2019-05-16 criteria provided, single submitter clinical testing

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