NM_001242896.3:c.791G>A
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4BS2
The NM_001242896.3(DEPDC5):c.791G>A(p.Arg264Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,774 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
Publications
- epilepsy, familial focal, with variable foci 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics, Illumina, G2P
- focal epilepsyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- autosomal dominant epilepsy with auditory featuresInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- autosomal dominant nocturnal frontal lobe epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial focal epilepsy with variable fociInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Brugada syndromeInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.791G>A | p.Arg264Lys | missense_variant | Exon 13 of 43 | NM_001242896.3 | ENSP00000498382.1 | |||
ENSG00000285404 | ENST00000646701.1 | c.707G>A | p.Arg236Lys | missense_variant | Exon 11 of 21 | ENSP00000496158.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152138Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000120 AC: 3AN: 249164 AF XY: 0.0000148 show subpopulations
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461636Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727132 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152138Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74320 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Epilepsy, familial focal, with variable foci 1 Uncertain:1
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Inborn genetic diseases Uncertain:1
The c.791G>A (p.R264K) alteration is located in exon 13 (coding exon 12) of the DEPDC5 gene. This alteration results from a G to A substitution at nucleotide position 791, causing the arginine (R) at amino acid position 264 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Familial focal epilepsy with variable foci Uncertain:1
This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 264 of the DEPDC5 protein (p.Arg264Lys). This variant is present in population databases (rs750467533, gnomAD 0.01%). 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: 579549). 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