X-66605180-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021783.5(EDA2R):c.134C>T(p.Pro45Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,207,947 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.0000055 ( 0 hom. 1 hem. )
Consequence
EDA2R
NM_021783.5 missense
NM_021783.5 missense
Scores
10
7
Clinical Significance
Conservation
PhyloP100: 3.00
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EDA2R | ENST00000374719.8 | c.134C>T | p.Pro45Leu | missense_variant | 3/7 | 1 | NM_021783.5 | ENSP00000363851.3 | ||
EDA2R | ENST00000253392.5 | c.134C>T | p.Pro45Leu | missense_variant | 2/6 | 1 | ENSP00000253392.5 | |||
EDA2R | ENST00000396050.5 | c.134C>T | p.Pro45Leu | missense_variant | 2/7 | 5 | ENSP00000379365.2 | |||
EDA2R | ENST00000451436.6 | c.134C>T | p.Pro45Leu | missense_variant | 3/7 | 5 | ENSP00000415242.3 |
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 3AN: 111704Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33862
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GnomAD3 exomes AF: 0.0000112 AC: 2AN: 177790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62956
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GnomAD4 exome AF: 0.00000547 AC: 6AN: 1096243Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 1AN XY: 361879
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GnomAD4 genome AF: 0.0000269 AC: 3AN: 111704Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33862
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.134C>T (p.P45L) alteration is located in exon 2 (coding exon 2) of the EDA2R gene. This alteration results from a C to T substitution at nucleotide position 134, causing the proline (P) at amino acid position 45 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
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
Uncertain
D
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.;D
REVEL
Benign
Sift
Uncertain
D;D;.;D
Sift4G
Uncertain
T;T;T;T
Polyphen
D;D;D;D
Vest4
MutPred
Loss of disorder (P = 0.034);Loss of disorder (P = 0.034);Loss of disorder (P = 0.034);Loss of disorder (P = 0.034);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at