X-48523796-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_006579.3(EBP):c.25C>T(p.His9Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H9Q) has been classified as Likely benign.
Frequency
Consequence
NM_006579.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.25C>T | p.His9Tyr | missense_variant | Exon 2 of 5 | ENST00000495186.6 | NP_006570.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.25C>T | p.His9Tyr | missense_variant | Exon 2 of 5 | 1 | NM_006579.3 | ENSP00000417052.1 | ||
ENSG00000286268 | ENST00000651615.1 | c.25C>T | p.His9Tyr | missense_variant | Exon 2 of 7 | ENSP00000498524.1 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
Chondrodysplasia punctata 2 X-linked dominant;C4085243:MEND syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.