COL11A2 p.Thr1561=
c.4683A>G · rs34055850 · VCV162976
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -3.7 |
| Overall | ||
| CADD | 0.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.193% | 519 |
| Finnishnot grpmax-eligible | 0.174% | 576 |
| European (non-Finnish)grpmax | 0.117% | 851 |
| Remaining individualsnot grpmax-eligible | 0.0864% | 1,157 |
| South Asian | 0.0275% | 3,643 |
| Admixed American | 0.0167% | 6,002 |
| African / African-American | 0.0107% | 9,375 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Thr1561=
- Coding
- c.4683A>G
- MANE Select
- NM_080680
- dbSNP
- rs34055850
- Type
- single nucleotide variant
- Location
- chr6:33165616 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
- Residue 1561
- the fibrillar collagen nc1 domain
Disease context
fibrochondrogenesis 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: otospondylomegaepiphyseal dysplasia, autosomal recessive
For Fibrochondrogenesis (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Neonatal
Similar variants
- COL11A2 p.Thr1561Ala Uncertain significance ★ ⚠ same residue
- COL11A2 p.Arg1020Ter Pathogenic/Likely pathogenic ★★ same condition
- COL11A2 p.Arg1331Ter Pathogenic ★★ same condition
- COL11A2 p.Arg1600Ter Pathogenic/Likely pathogenic ★★ same condition
- COL11A2 p.Arg433Ter Pathogenic/Likely pathogenic ★★ same condition
- COL11A2 p.Arg558Ter Pathogenic ★★ same condition
- COL11A2 p.Gly1027Glu Likely pathogenic ★★ same condition
- COL11A2 c.2682+5G>A Uncertain significance ★★ 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/col11a2-p-thr1561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown