COL11A2 p.Pro879=
c.2637T>C · rs199677738 · VCV597024
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0189%, mid)
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 -0.26 | GERP -1.7, phastCons 0.001 |
| Overall | ||
| CADD | 10.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0189%
Middle Eastern · 1/5,290 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00362%
Overall
0.00101%
15/1,488,128 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0189% | 5,290 |
| African / African-American | 0.011% | 9,122 |
| Remaining individualsnot grpmax-eligible | 0.00539% | 18,554 |
| South Asian | 0.00337% | 29,706 |
| Admixed American | 0.00192% | 52,190 |
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.Pro879=
- Coding
- c.2637T>C
- MANE Select
- NM_080680
- dbSNP
- rs199677738
- Type
- single nucleotide variant
- Location
- chr6:33173547 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
- Residue 879
- the 'disordered' region; the 'triple-helical region' region; a UniProt-annotated variant site (in); the collagen-like 5 domain
Similar variants
- COL11A2 p.Pro879Ser Uncertain significance ★ ⚠ same residue
- COL11A2 c.1119+1G>A Likely pathogenic ★★ same type
- COL11A2 c.1819-2A>G Likely pathogenic ★★ same type
- COL11A2 c.3852+1G>T Likely pathogenic ★★ same type
- COL11A2 c.4392+1G>A Pathogenic ★★ same type
- COL11A2 c.607-2A>T Likely pathogenic ★★ same type
- COL11A2 c.876+1G>A Likely pathogenic ★★ same type
- COL11A2 p.Arg1020Ter 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/col11a2-p-pro879 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown