COL10A1 p.Pro149=
c.447G>A · rs560942887 · VCV1022305
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
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 -11 | GERP -3.9 |
| Overall | ||
| CADD | 0.666 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/60,016 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.00397%
64/1,613,800 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 5,001 |
| African / African-American | 0.0173% | 5,770 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,926 |
| European (non-Finnish) | 0.00246% | 40,682 |
| East Asian | 0.00223% | 44,858 |
| Finnishnot grpmax-eligible | 0.00156% | 64,010 |
| South Asian | 0.0011% | 91,064 |
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
- COL10A1
- Protein
- p.Pro149=
- Coding
- c.447G>A
- MANE Select
- NM_000493
- dbSNP
- rs560942887
- Type
- single nucleotide variant
- Location
- chr6:116121669 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 58.80 · 1 PDB
- Residue 149
- the 'disordered' region; the 'triple-helical region' region
Similar variants
- COL10A1 p.Pro149Leu Uncertain significance ★ ⚠ same residue
- COL10A1 p.Arg71Ter Pathogenic/Likely pathogenic ★★ same type
- COL10A1 p.Cys591Arg Likely pathogenic ★★ same type
- COL10A1 p.Gln653Ter Pathogenic/Likely pathogenic ★★ same type
- COL10A1 p.Gly18Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- COL10A1 p.Gly18Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
- COL10A1 p.Ser671Pro Pathogenic/Likely pathogenic ★★ same type
- COL10A1 p.Tyr597His 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/col10a1-p-pro149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown