DEPDC5 p.Phe164del
c.489_491del · rs587776974 · VCV50821
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
2
DEPDC5-related disorder
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 12 | GERP 4.3, phastCons 1 |
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.Phe164del
- Coding
- c.489_491del
- MANE Select
- NM_001242896
- dbSNP
- rs587776974
- Type
- Deletion
- Location
- chr22:31783911 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.22 · 11 PDB
- Residue 164
- a β-strand
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.Val340fs Pathogenic/Likely pathogenic ★★ same condition
- DEPDC5 p.Phe164Val Uncertain significance ★★ ⚠ same residue
- DEPDC5 c.1325-6_1325-1del Likely pathogenic ★ same condition
- DEPDC5 c.4204del Pathogenic ★ same condition
- DEPDC5 p.Ala1489fs 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-phe164del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown