rs121908455
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_022336.4(EDAR):c.329A>C(p.Asp110Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D110N) has been classified as Uncertain significance.
Frequency
Consequence
NM_022336.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDAR | NM_022336.4 | c.329A>C | p.Asp110Ala | missense_variant | 4/12 | ENST00000258443.7 | |
EDAR | XM_006712204.2 | c.329A>C | p.Asp110Ala | missense_variant | 4/11 | ||
RANBP2 | XM_047445367.1 | c.8370+156179T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDAR | ENST00000258443.7 | c.329A>C | p.Asp110Ala | missense_variant | 4/12 | 1 | NM_022336.4 | P1 | |
EDAR | ENST00000376651.1 | c.329A>C | p.Asp110Ala | missense_variant | 4/11 | 2 | |||
EDAR | ENST00000409271.5 | c.329A>C | p.Asp110Ala | missense_variant | 5/12 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251246Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135858
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461770Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727184
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Ectodermal dysplasia 10B, hypohidrotic/hair/tooth type, autosomal recessive Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at