chrX-66604439-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021783.5(EDA2R):c.334C>G(p.Pro112Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 22)
Consequence
EDA2R
NM_021783.5 missense
NM_021783.5 missense
Scores
2
8
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.18
Genes affected
EDA2R (HGNC:17756): (ectodysplasin A2 receptor) The protein encoded by this gene is a type III transmembrane protein of the TNFR (tumor necrosis factor receptor) superfamily, and contains cysteine-rich repeats and a single transmembrane domain. This protein binds to the EDA-A2 isoform of ectodysplasin, which plays an important role in maintenance of hair and teeth. Alternatively spliced transcript variants encodes distinct protein isoforms. [provided by RefSeq, Apr 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EDA2R | ENST00000374719.8 | c.334C>G | p.Pro112Ala | missense_variant | Exon 4 of 7 | 1 | NM_021783.5 | ENSP00000363851.3 | ||
EDA2R | ENST00000253392.5 | c.334C>G | p.Pro112Ala | missense_variant | Exon 3 of 6 | 1 | ENSP00000253392.5 | |||
EDA2R | ENST00000396050.5 | c.334C>G | p.Pro112Ala | missense_variant | Exon 3 of 7 | 5 | ENSP00000379365.2 | |||
EDA2R | ENST00000451436.6 | c.334C>G | p.Pro112Ala | missense_variant | Exon 4 of 7 | 5 | ENSP00000415242.3 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
Cov.:
22
GnomAD3 exomes AF: 0.00000553 AC: 1AN: 180972Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65624
GnomAD3 exomes
AF:
AC:
1
AN:
180972
Hom.:
AF XY:
AC XY:
0
AN XY:
65624
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
ExAC
AF:
AC:
1
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;.;D;.
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
.;D;D;.
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;.;D
REVEL
Benign
Sift
Uncertain
D;D;.;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
P;D;P;D
Vest4
MutPred
Loss of glycosylation at P112 (P = 0.0255);Loss of glycosylation at P112 (P = 0.0255);Loss of glycosylation at P112 (P = 0.0255);Loss of glycosylation at P112 (P = 0.0255);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at