rs778753730
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_001242896.3(DEPDC5):c.3014T>A(p.Met1005Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,494 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
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.3014T>A | p.Met1005Lys | missense_variant | Exon 30 of 43 | NM_001242896.3 | ENSP00000498382.1 | |||
ENSG00000285404 | ENST00000646701.1 | c.1786+26005T>A | intron_variant | Intron 20 of 20 | ENSP00000496158.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152272Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000971 AC: 24AN: 247076Hom.: 0 AF XY: 0.0000596 AC XY: 8AN XY: 134246
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461222Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726862
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152272Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74390
ClinVar
Submissions by phenotype
Familial focal epilepsy with variable foci Uncertain:1
This sequence change replaces methionine, which is neutral and non-polar, with lysine, which is basic and polar, at codon 1005 of the DEPDC5 protein (p.Met1005Lys). This variant is present in population databases (rs778753730, gnomAD 0.07%). This variant has not been reported in the literature in individuals affected with DEPDC5-related conditions. ClinVar contains an entry for this variant (Variation ID: 568881). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at