Is DEPDC5 p.Ser1154Phe (c.3461C>T) pathogenic?

DEPDC5 p.Ser1154Phe (c.3461C>T) is classified Uncertain significance in DEPDC5 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2025-09-10). AlphaMissense: likely benign (0.092); Ultra-rare (popmax 0.0115%, nfe); Associated with familial focal epilepsy with variable foci.

What condition is associated with DEPDC5 p.Ser1154Phe (c.3461C>T)?

DEPDC5 p.Ser1154Phe (c.3461C>T) is associated with familial focal epilepsy with variable foci, epilepsy, familial focal, with variable foci 1 (ClinVar).

How common is DEPDC5 p.Ser1154Phe (c.3461C>T) in the general population?

DEPDC5 p.Ser1154Phe (c.3461C>T) is ultra-rare (popmax 0.0115%, nfe) (gnomAD).

How is Familial focal epilepsy with variable foci inherited?

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

What do computational predictors say about DEPDC5 p.Ser1154Phe (c.3461C>T)?

AlphaMissense predicts likely benign (score 0.092) — an in-silico prediction, not a clinical call.

DEPDC5 p.Ser1154Phe

c.3461C>T · rs578244490 · VCV264763

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.092 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0115%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

familial focal epilepsy with variable foci

Computational evidence

Protein change
AlphaMissense	0.092	likely benign
REVEL	0.025	moderately benign-leaning
SaProt	LLR -8.13	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP 3.7, phastCons 0.003
Regional constraint	o/e 0.97	unconstrained · MANE · 8,920 bp · p 0.7 · regional, not allelic
Overall
CADD	21.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0115% European (non-Finnish) · 134/1,167,628 alleles

Filtering AF 0.00988% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00928%

Overall 0.00878% 139/1,583,666 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0115%	8,714
Remaining individualsnot grpmax-eligible	0.00654%	15,288
African / African-American	0.00136%	73,352

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DEPDC5
Protein: p.Ser1154Phe
Coding: c.3461C>T
MANE Select: NM_001242896
dbSNP: rs578244490
Type: single nucleotide variant
Location: chr22:31870720 (GRCh38)
Gene constraint: LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.22 · 11 PDB
Residue 1154: a UniProt-annotated variant site (in ffevf1; uncertain significance); the 'disordered' region

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

Also linked: epilepsy, familial focal, with variable foci 1

For Familial focal epilepsy with variable foci (Orphanet):

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

Similar variants

DEPDC5 c.1218-1G>A Pathogenic ★★ same condition
DEPDC5 c.1287+1G>A Pathogenic/Likely pathogenic ★★ same condition
DEPDC5 c.1324+1G>A Likely pathogenic ★★ same condition
DEPDC5 c.1324+1G>T Likely pathogenic ★★ same condition
DEPDC5 c.193+1G>T Pathogenic/Likely pathogenic ★★ same condition
DEPDC5 c.2105-1G>A Likely pathogenic ★★ same condition
DEPDC5 c.2634-2A>G Likely pathogenic ★★ same condition
DEPDC5 c.280-1G>A Pathogenic/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-p-ser1154phe (accessed [today's date]).

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