COL2A1 p.Glu487Ter
c.1458dup · VCV4734309
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 23 of 54 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- COL2A1
- Protein
- p.Glu487Ter
- Coding
- c.1458dup
- MANE Select
- NM_001844
- Type
- Duplication
- Location
- chr12:47986404 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 11 PDB
- Residue 487
- an α-helix; the 'disordered' region; the 'triple-helical region' region
Similar variants
- COL2A1 c.1680+2dup Pathogenic/Likely pathogenic ★★ same type
- COL2A1 c.1681-1dup Pathogenic ★★ same type
- COL2A1 c.2094_2094+1dup Pathogenic/Likely pathogenic ★★ same type
- COL2A1 p.Ala895fs Pathogenic ★★ same type
- COL2A1 p.Gly741fs Pathogenic ★★ same type
- COL2A1 p.Gly795fs Pathogenic ★★ same type
- COL2A1 p.Gly909fs Pathogenic ★★ same type
- COL2A1 p.Ile1180fs 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/col2a1-p-glu487ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown