Is DEPDC5 p.Arg1007Trp (c.3019C>T) pathogenic?

DEPDC5 p.Arg1007Trp (c.3019C>T) is classified Uncertain significance in DEPDC5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-04). AlphaMissense: likely pathogenic (0.8077); Very rare (popmax 0.00133%, afr); Associated with familial focal epilepsy with variable foci.

What condition is associated with DEPDC5 p.Arg1007Trp (c.3019C>T)?

DEPDC5 p.Arg1007Trp (c.3019C>T) is associated with familial focal epilepsy with variable foci (ClinVar).

How common is DEPDC5 p.Arg1007Trp (c.3019C>T) in the general population?

DEPDC5 p.Arg1007Trp (c.3019C>T) is very rare (popmax 0.00133%, afr) (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.Arg1007Trp (c.3019C>T)?

AlphaMissense predicts likely pathogenic (score 0.8077) — an in-silico prediction, not a clinical call.

DEPDC5 p.Arg1007Trp

c.3019C>T · rs1283955876 · VCV939121

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.8077 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

familial focal epilepsy with variable foci

Computational evidence

Protein change
AlphaMissense	0.8077	likely pathogenic
REVEL	0.305	indeterminate
SaProt	LLR -9.21	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	Δ0.83	donor gain · deltas
Constraint at this position
Conservation	phyloP 2.6	GERP 3.7, phastCons 0.99
Regional constraint	o/e 0.76	unconstrained · MANE · 9,878 bp · p 2.2e-06 · regional, not allelic
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,920 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000558% 9/1,612,604 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	74,920
South Asian	0.0011%	90,818
European (non-Finnish)	0.000594%	168,484

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.Arg1007Trp
Coding: c.3019C>T
MANE Select: NM_001242896
dbSNP: rs1283955876
Type: single nucleotide variant
Location: chr22:31845235 (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.Arg1007= Conflicting classifications of pathogenicity ★ same residue
DEPDC5 p.Arg1007Gln Uncertain significance ★ ⚠ same residue
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

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-arg1007trp (accessed [today's date]).

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