DEPDC5 p.Ala464fs
c.1391_1398del · VCV4072054
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
epilepsy, familial focal, with variable foci 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 20 of 43 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -4.8 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- DEPDC5
- Protein
- p.Ala464fs
- Coding
- c.1391_1398del
- MANE Select
- NM_001242896
- Type
- Deletion
- Location
- chr22:31810586 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.22 · 11 PDB
- Residue 464
- a turn
Disease context
epilepsy, familial focal, with variable foci 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Familial focal epilepsy with variable foci (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Adult, Childhood, Infancy
Similar variants
- DEPDC5 p.Ala464Thr Uncertain significance ★ ⚠ same residue
- DEPDC5 p.Asn1362fs Pathogenic ★★ same condition
- DEPDC5 p.Lys229fs Pathogenic/Likely pathogenic ★★ same condition
- DEPDC5 p.Phe1384fs Likely pathogenic ★★ same condition
- DEPDC5 p.Phe164del Pathogenic ★★ same condition
- DEPDC5 p.Val340fs Pathogenic/Likely pathogenic ★★ same condition
- DEPDC5 c.1325-6_1325-1del Likely pathogenic ★ same condition
- DEPDC5 c.4204del Pathogenic ★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/depdc5-p-ala464fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown