COL2A1 c.654+5del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
1
Stickler syndrome, type I, nonsyndromic ocular
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +5 | donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
| Non-coding constraint | Z 3.41 | 1 kb window · o/e 0.74 · regional · uncalibrated |
Variant & gene context
- Gene
- COL2A1
- Coding
- c.654+5del
- MANE Select
- NM_001844
- Type
- Deletion
- Location
- chr12:47995870 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 11 PDB
Similar variants
- COL2A1 p.Pro953fs Pathogenic ★★ same condition
- COL2A1 p.Gly1446fs Uncertain significance ★ same condition
- COL2A1 p.Ala362_Pro365del Likely pathogenic same condition
- COL2A1 p.Glu232fs Pathogenic same condition
- COL2A1 c.1420-1G>A Pathogenic ★★ same condition
- COL2A1 c.1527+1G>A Likely pathogenic ★★ same condition
- COL2A1 p.Ala302Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- COL2A1 p.Arg565Cys Pathogenic/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/col2a1-c-654-plus-5del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown