X-69957097-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM5PP3PP5_Moderate
The NM_001399.5(EDA):c.467G>T(p.Arg156Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R156G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001399.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Hypohidrotic X-linked ectodermal dysplasia Pathogenic:1
The p.Arg156Leu variant in EDA has been reported in 1 adult male with X-linked h ypohidrotic ectodermal dysplasia (XLHED; Dietz 2013), and was absent from large population studies. In addition, several variants affecting the same amino acid position (p.Arg156His, p.Arg156Cys, p.Arg156Gly, p.Arg156Ser) have been identifi ed in multiple individuals with X-linked hypohidrotic ectodermal dysplasia and s egregated with disease in those families, suggesting that the arginine (Arg) res idue at position 156 is intolerant to variation (Monreal 1998, Aoki 2000, Schnei der 2001, Vincent 2001, Schneider 2011, Zhao 2008, Cluzeau 2011, Clauss 2010, Li 2013, He 2013, Dietz 2013). In vitro functional studies provide evidence that a change affecting this amino acid position disrupts the normal processing and fu nction of the EDA protein (Chen 2001), consistent with a causal role for variant s identified at this position. In summary, this variant meets our criteria to be classified as pathogenic for X-linked hypohidrotic ectodermal dysplasia (http:/ /www.partners.org/personalizedmedicine/LMM) based upon the presence of this vari ant as well as other variants affecting the same position in several affected in dividuals, and the functional evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at