Is DEPDC5 p.Phe601fs (c.1800del) pathogenic?

DEPDC5 p.Phe601fs (c.1800del) is classified Pathogenic in DEPDC5 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-01). Ultra-rare (gnomAD MAF 1.241e-06); Associated with familial focal epilepsy with variable foci.

What condition is associated with DEPDC5 p.Phe601fs (c.1800del)?

DEPDC5 p.Phe601fs (c.1800del) is associated with familial focal epilepsy with variable foci (ClinVar).

How common is DEPDC5 p.Phe601fs (c.1800del) in the general population?

DEPDC5 p.Phe601fs (c.1800del) is ultra-rare (gnomAD MAF 1.241e-06) (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.Phe601fs

c.1800del · rs2148802008 · VCV1454587

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (gnomAD MAF 1.241e-06)

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 22 of 43
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 4.1, phastCons 1

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

Population frequency

dbSNP / gnomAD

Global frequency 0.000124% via dbSNP · ultra-rare

No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.

Variant & gene context

Gene: DEPDC5
Protein: p.Phe601fs
Coding: c.1800del
MANE Select: NM_001242896
dbSNP: rs2148802008
Type: Deletion
Location: chr22:31819152 (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

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.Phe601= Likely benign ★★ 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-phe601fs (accessed [today's date]).

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