DRC1 p.Trp402Ter
c.1205G>A · VCV3342719
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 10 of 17 |
| Splicing | ||
| SpliceAI | Δ0.21 | acceptor loss, 41 bp away · masked 0 · deltas |
| Pangolin | Δ0.39 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 42.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,002 |
| African / African-American | 0.00133% | 74,912 |
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
- DRC1
- Protein
- p.Trp402Ter
- Coding
- c.1205G>A
- MANE Select
- NM_145038
- Type
- single nucleotide variant
- Location
- chr2:26444757 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.44 · 1 PDB
- Residue 402
- a UniProt-annotated variant site (in spgf80); a UniProt-annotated variant site (in cild21)
Similar variants
- DRC1 p.Trp402Cys Uncertain significance ★★ ⚠ same residue
- DRC1 p.Gln118Ter Pathogenic/Likely pathogenic ★★ same type
- DRC1 p.Gln337Ter Pathogenic/Likely pathogenic ★★ same type
- DRC1 p.Ser642Ter Pathogenic/Likely pathogenic ★★ same type
- DRC1 p.Ala250Val Uncertain significance ★★ ⚠ same type
- DRC1 p.Ala391Val Uncertain significance ★★ ⚠ same type
- DRC1 p.Ala416Gly Uncertain significance ★★ ⚠ same type
- DRC1 p.Ala45Val Uncertain significance ★★ ⚠ same type
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/drc1-p-trp402ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown