DEPDC5 p.Val1417=
c.4251C>T · rs762073691 · VCV1739098
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.038 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP 1.9 |
| Overall | ||
| CADD | 5.829 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,080 alleles
Overall
6.84e-05%
1/1,461,778 alleles · very rare
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.Val1417=
- Coding
- c.4251C>T
- MANE Select
- NM_001242896
- dbSNP
- rs762073691
- Type
- single nucleotide variant
- Location
- chr22:31897529 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.22 · 11 PDB
- Residue 1417
- a β-strand
Similar variants
- 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
- DEPDC5 c.2634-2A>G 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-val1417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown