DEPDC5 p.Asp678=
c.2034C>T · rs779428450 · VCV466462
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.096 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.38 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.13 | GERP 0.97, phastCons 0.003 |
| Overall | ||
| CADD | 10.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,004 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00455%
Overall
0.00508%
82/1,614,008 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,572 |
| European (non-Finnish) | 0.0061% | 16,389 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00133% | 74,928 |
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.Asp678=
- Coding
- c.2034C>T
- MANE Select
- NM_001242896
- dbSNP
- rs779428450
- Type
- single nucleotide variant
- Location
- chr22:31822720 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.22 · 11 PDB
Similar variants
- DEPDC5 p.Asp678Asn Uncertain significance ★★ ⚠ same residue
- DEPDC5 c.1217+1G>A Likely pathogenic ★★ same condition
- 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-asp678 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown