rs397516673
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_001399.5(EDA):c.740A>G(p.Gln247Arg) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 2/2 splice prediction tools predicting alterations to normal splicing. 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. Q247H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001399.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDA | NM_001399.5 | c.740A>G | p.Gln247Arg | missense_variant, splice_region_variant | 5/8 | ENST00000374552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDA | ENST00000374552.9 | c.740A>G | p.Gln247Arg | missense_variant, splice_region_variant | 5/8 | 1 | NM_001399.5 | P4 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 20, 2011 | The Gln247Arg variant in EDA has not been reported in the literature nor previou sly identified by our laboratory. The amino acid glutamine (Gln) at position 24 7 is highly conserved across evolutionarily distant species, suggesting that a c hange to the amino acid arginine (Arg) may not be tolerated. Computational anal yses (biochemical amino acid properties, homology, PolyPhen2, SIFT, AlignGVGD) d o not provide strong support for or against pathogenicity. Without further info rmation, such as control studies, segregation data, or functional analyses, the clinical significance of this variant cannot be determined with certainty at thi s time. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at