VCP p.Arg453=
c.1359G>A · rs2490353756 · VCV1710642
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.91 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.70 | gain · loss 0.31 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 0.47, phastCons 1 |
| Overall | ||
| CADD | 25.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- VCP
- Protein
- p.Arg453=
- Coding
- c.1359G>A
- MANE Select
- NM_007126
- dbSNP
- rs2490353756
- Type
- single nucleotide variant
- Location
- chr9:35061015 (GRCh38)
- Gene constraint
- LOEUF 0.134 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.11 · 144 PDB
- Residue 453
- an α-helix
Similar variants
- VCP p.Arg453Gln Uncertain significance ★★ ⚠ same residue
- VCP p.Arg453Trp Uncertain significance ★★ ⚠ same residue
- VCP p.Arg155Cys Pathogenic/Likely pathogenic ★★ same type
- VCP p.Arg155Gly Pathogenic/Likely pathogenic ★★ same type
- VCP p.Arg155His Pathogenic ★★ ⚠ same type
- VCP p.Arg159Cys Pathogenic/Likely pathogenic ★★ same type
- VCP p.Arg159His Pathogenic ★★ same type
- VCP p.Arg191Gln Pathogenic/Likely pathogenic ★★ 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/vcp-p-arg453 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown