COL11A2 p.Gln97=
c.291A>G · rs538869102 · VCV1200313
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 0.0547%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.35 | GERP -3.4, phastCons 0.084 |
| Overall | ||
| CADD | 13.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0547%
African / African-American · 41/74,984 alleles
Filtering AF
0.0413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0367%
Overall
0.00353%
57/1,613,988 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0547% | 1,829 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| East Asian | 0.00223% | 44,878 |
| South Asian | 0.0022% | 45,539 |
| Admixed American | 0.00167% | 60,014 |
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.Gln97=
- Coding
- c.291A>G
- MANE Select
- NM_080680
- dbSNP
- rs538869102
- Type
- single nucleotide variant
- Location
- chr6:33189130 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
- Residue 97
- the laminin g-like domain
Similar variants
- 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
- COL11A2 p.Arg1034Cys 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-gln97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown