COL11A1 p.Ser415=
c.1245C>T · rs371490794 · VCV386500
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 0.069 | GERP -2.2, phastCons 0.42 |
| Overall | ||
| CADD | 9.027 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,870 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000744%
12/1,613,306 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,478 |
| East Asian | 0.00223% | 44,850 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000339% | 294,978 |
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.Ser415=
- Coding
- c.1245C>T
- MANE Select
- NM_001854
- dbSNP
- rs371490794
- Type
- single nucleotide variant
- Location
- chr1:103022742 (GRCh38)
- Gene constraint
- LOEUF 0.349 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 53.06
- Residue 415
- the 'nonhelical region' region
Similar variants
- COL11A1 p.Ser415Arg Uncertain significance ★★ ⚠ same residue
- COL11A1 p.Ser415Asn 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
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-ser415 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown