X-69616367-G-GAGGGAGCC
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001399.5(EDA):c.64_71dupAGCCAGGG(p.Cys25AlafsTer35) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_001399.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Hypohidrotic X-linked ectodermal dysplasia Pathogenic:2
This sequence change creates a premature translational stop signal (p.Cys25Alafs*35) in the EDA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EDA are known to be pathogenic (PMID: 9683615). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with ectodermal dysplasia (PMID: 27305980). ClinVar contains an entry for this variant (Variation ID: 2737241). For these reasons, this variant has been classified as Pathogenic. -
PVS1+PM2_Supporting+PS4_Moderate+PP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.