NM_001242896.3:c.268G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001242896.3(DEPDC5):c.268G>A(p.Val90Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000744 in 1,612,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001242896.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.268G>A | p.Val90Ile | missense_variant | Exon 5 of 43 | NM_001242896.3 | ENSP00000498382.1 | |||
ENSG00000285404 | ENST00000646701.1 | c.268G>A | p.Val90Ile | missense_variant | Exon 4 of 21 | ENSP00000496158.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249488Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135356
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460564Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 726634
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
Self-limited epilepsy with centrotemporal spikes Pathogenic:1
CAADphred>15 -
Familial focal epilepsy with variable foci Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 90 of the DEPDC5 protein (p.Val90Ile). This variant is present in population databases (rs768456731, gnomAD 0.003%). This missense change has been observed in individual(s) with Rolandic epilepsy (PMID: 24591017). ClinVar contains an entry for this variant (Variation ID: 264750). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this missense change does not substantially affect DEPDC5 function (PMID: 25366275). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Epilepsy, familial focal, with variable foci 1 Other:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at