COL11A2 p.Arg110Pro
c.329G>C · rs145960317 · VCV2975685
Computational evidence
| Protein change | ||
| AlphaMissense | 0.149 | likely benign |
|---|---|---|
| REVEL | 0.422 | indeterminate |
| SaProt | LLR -6.12 | tolerated |
| ⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.22 | GERP -3.7, phastCons 0.014 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 29 kb · p 3e-20 · regional, not allelic |
| Overall | ||
| CADD | 14.12 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
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
- COL11A2
- Protein
- p.Arg110Pro
- Coding
- c.329G>C
- MANE Select
- NM_080680
- dbSNP
- rs145960317
- Type
- single nucleotide variant
- Location
- chr6:33189092 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
- Residue 110
- the laminin g-like domain
Disease context
otospondylomegaepiphyseal dysplasia, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal recessive otospondylomegaepiphyseal dysplasia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Neonatal
Similar variants
- COL11A2 p.Arg110Ter Pathogenic ★★ same residue
- COL11A2 p.Arg110Gln Benign/Likely benign ★★ same residue
- COL11A2 c.4392+1G>A Pathogenic ★★ same condition
- COL11A2 p.Arg1020Ter Pathogenic/Likely pathogenic ★★ same condition
- COL11A2 p.Arg1331Ter Pathogenic ★★ same condition
- COL11A2 p.Arg1379Ter Pathogenic/Likely pathogenic ★★ same condition
- COL11A2 p.Arg1600Ter Pathogenic/Likely pathogenic ★★ same condition
- COL11A2 p.Arg379Ter 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/col11a2-p-arg110pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown