COL11A1 p.Pro840=
c.2520A>G · rs942911563 · VCV1195718
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0067%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.087 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 10.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0067%
Admixed American · 4/59,742 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000375%
6/1,599,346 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0067% | 14,935 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,924 |
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
- COL11A1
- Protein
- p.Pro840=
- Coding
- c.2520A>G
- MANE Select
- NM_001854
- dbSNP
- rs942911563
- Type
- single nucleotide variant
- Location
- chr1:102984174 (GRCh38)
- Gene constraint
- LOEUF 0.349 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 53.06
- Residue 840
- the 'disordered' region; the 'triple-helical region' region
Similar variants
- COL11A1 p.Pro840Ala Uncertain significance ★ ⚠ same residue
- COL11A1 c.1245+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL11A1 c.1245+1G>T Pathogenic/Likely pathogenic ★★ same type
- COL11A1 c.1629+1G>A Likely pathogenic ★★ same type
- COL11A1 c.1630-1G>T Pathogenic ★★ same type
- COL11A1 c.1791+1G>T Likely pathogenic ★★ same type
- COL11A1 c.1900-1G>A Likely pathogenic ★★ same type
- COL11A1 c.2241+5G>T Pathogenic/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/col11a1-p-pro840 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown