COL11A2 p.Ile1506fs
c.4515dup · rs2534465587 · VCV2713919
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 63 of 66 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- COL11A2
- Protein
- p.Ile1506fs
- Coding
- c.4515dup
- MANE Select
- NM_080680
- dbSNP
- rs2534465587
- Type
- Duplication
- Location
- chr6:33165783 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
- Residue 1506
- the 'disordered' region
Similar variants
- COL11A2 p.Ile1506Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL11A2 c.1719+3dup Likely pathogenic ★★ same type
- COL11A2 p.Ala23fs Pathogenic ★★ same type
- COL11A2 p.Gly1111fs Pathogenic/Likely pathogenic ★★ same type
- COL11A2 p.Gly1183fs Pathogenic/Likely pathogenic ★★ same type
- COL11A2 p.Gly1279fs Pathogenic/Likely pathogenic ★★ same type
- COL11A2 p.Pro340_Glu341insTer Pathogenic/Likely pathogenic ★★ same type
- COL11A2 p.Pro950fs 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/col11a2-p-ile1506fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown