Is DEPDC5 c.4204del pathogenic?

DEPDC5 c.4204del is classified Pathogenic in DEPDC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-01). Associated with epilepsy, familial focal, with variable foci 1.

What condition is associated with DEPDC5 c.4204del?

DEPDC5 c.4204del is associated with epilepsy, familial focal, with variable foci 1 (ClinVar).

How is Familial focal epilepsy with variable foci inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

DEPDC5 c.4204del

VCV4683087

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

epilepsy, familial focal, with variable foci 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 4, phastCons 1
Non-coding constraint	Z 2.58	1 kb window · o/e 0.81 · regional · uncalibrated

Variant & gene context

Gene: DEPDC5
Coding: c.4204del
MANE Select: NM_001242896
Type: Deletion
Location: chr22:31897481 (GRCh38)
Gene constraint: LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.22 · 11 PDB

Full DEPDC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

epilepsy, familial focal, with variable foci 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial focal epilepsy with variable foci (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood, Infancy

Similar variants

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 p.Ala1489fs Likely pathogenic ★ same condition
DEPDC5 p.Ala426fs Likely 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-c-4204del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown