rs587776975
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001242896.3(DEPDC5):c.4107G>A(p.Trp1369Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001242896.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DEPDC5 | NM_001242896.3 | c.4107G>A | p.Trp1369Ter | stop_gained | 39/43 | ENST00000651528.2 | NP_001229825.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.4107G>A | p.Trp1369Ter | stop_gained | 39/43 | NM_001242896.3 | ENSP00000498382 | P4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461746Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727178
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Epilepsy, familial focal, with variable foci 1 Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 09, 2014 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Autosomal dominant epilepsy Pathogenic:1
Pathogenic, no assertion criteria provided | research | Rare Disease Center, Seoul National University Hospital | Mar 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at