chrX-66604439-G-C

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

Scores

2
8
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.18
Variant links:
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]

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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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EDA2RNM_021783.5 linkc.334C>G p.Pro112Ala missense_variant Exon 4 of 7 ENST00000374719.8 NP_068555.2 Q9HAV5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EDA2RENST00000374719.8 linkc.334C>G p.Pro112Ala missense_variant Exon 4 of 7 1 NM_021783.5 ENSP00000363851.3 Q9HAV5-1
EDA2RENST00000253392.5 linkc.334C>G p.Pro112Ala missense_variant Exon 3 of 6 1 ENSP00000253392.5 Q9HAV5-2
EDA2RENST00000396050.5 linkc.334C>G p.Pro112Ala missense_variant Exon 3 of 7 5 ENSP00000379365.2 Q9HAV5-2
EDA2RENST00000451436.6 linkc.334C>G p.Pro112Ala missense_variant Exon 4 of 7 5 ENSP00000415242.3 Q9HAV5-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD3 exomes
AF:
0.00000553
AC:
1
AN:
180972
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
65624
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000124
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
22
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.40
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.51
D;.;D;.
FATHMM_MKL
Benign
0.73
D
LIST_S2
Uncertain
0.86
.;D;D;.
M_CAP
Benign
0.070
D
MetaRNN
Uncertain
0.54
D;D;D;D
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.2
M;M;M;M
PrimateAI
Uncertain
0.59
T
PROVEAN
Pathogenic
-6.1
D;D;.;D
REVEL
Benign
0.20
Sift
Uncertain
0.0040
D;D;.;D
Sift4G
Pathogenic
0.0
D;D;D;D
Polyphen
0.92
P;D;P;D
Vest4
0.43
MutPred
0.69
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
0.19
ClinPred
0.73
D
GERP RS
3.4
Varity_R
0.37
gMVP
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12837393; hg19: chrX-65824281; API