Is DEPDC5 p.Asp113fs (c.338del) pathogenic?

DEPDC5 p.Asp113fs (c.338del) is classified Pathogenic in DEPDC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-28). Absent from gnomAD; Associated with familial focal epilepsy with variable foci.

What condition is associated with DEPDC5 p.Asp113fs (c.338del)?

DEPDC5 p.Asp113fs (c.338del) is associated with familial focal epilepsy with variable foci (ClinVar).

How common is DEPDC5 p.Asp113fs (c.338del) in the general population?

DEPDC5 p.Asp113fs (c.338del) is absent from gnomAD (gnomAD).

How is Familial focal epilepsy with variable foci inherited?

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

DEPDC5 p.Asp113fs

c.338del · rs2517947003 · VCV2011937

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

familial focal epilepsy with variable foci

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 6 of 43
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 3.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DEPDC5
Protein: p.Asp113fs
Coding: c.338del
MANE Select: NM_001242896
dbSNP: rs2517947003
Type: Deletion
Location: chr22:31766643 (GRCh38)
Gene constraint: LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.22 · 11 PDB
Residue 113: an α-helix

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

Disease context

familial focal epilepsy with variable foci — 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.Asp113Val Uncertain significance ★★ ⚠ same residue
DEPDC5 p.Asn1362fs Pathogenic ★★ same condition
DEPDC5 p.Asn437fs Pathogenic ★★ same condition
DEPDC5 p.Gly1564_Asp1565insTer Pathogenic/Likely pathogenic ★★ same condition
DEPDC5 p.Pro1309fs Pathogenic ★★ same condition
DEPDC5 p.Ser386fs Pathogenic/Likely pathogenic ★★ same condition
DEPDC5 p.Val340fs Pathogenic/Likely pathogenic ★★ same condition
DEPDC5 c.1218-5del Benign/Likely benign ★★ 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-asp113fs (accessed [today's date]).

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