COL11A2 p.Ser1452=
c.4356C>T · rs199515114 · VCV513005
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0557%, eas)
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 -0.17 | GERP -2.8, phastCons 0.004 |
| Overall | ||
| CADD | 10.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0557%
East Asian · 25/44,880 alleles
Filtering AF
0.0387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.033%
Overall
0.00496%
80/1,613,722 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0557% | 1,795 |
| Middle Eastern | 0.0164% | 6,082 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,496 |
| European (non-Finnish) | 0.00373% | 26,815 |
| South Asian | 0.00329% | 30,361 |
| African / African-American | 0.00267% | 37,425 |
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.Ser1452=
- Coding
- c.4356C>T
- MANE Select
- NM_080680
- dbSNP
- rs199515114
- Type
- single nucleotide variant
- Location
- chr6:33166549 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
- Residue 1452
- the collagen-like 8 domain; the 'disordered' region; the 'triple-helical region' region
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-ser1452 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown