COL9A3 p.Pro147=
c.441C>T · rs41306378 · VCV1569690
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00988%, nfe)
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 -0.67 | GERP -2 |
| Overall | ||
| CADD | 6.969 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
European (non-Finnish) · 114/1,153,960 alleles
Filtering AF
0.00836%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00778%
Overall
0.00776%
123/1,584,418 alleles · very rare
exomes 111/1,432,426 · genomes 12/151,992 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00988% | 10,122 |
| Remaining individualsnot grpmax-eligible | 0.00975% | 10,252 |
| South Asian | 0.00221% | 45,261 |
| Admixed American | 0.00167% | 59,944 |
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
- COL9A3
- Protein
- p.Pro147=
- Coding
- c.441C>T
- MANE Select
- NM_001853
- dbSNP
- rs41306378
- Type
- single nucleotide variant
- Location
- chr20:62822128 (GRCh38)
- Gene constraint
- LOEUF 1.026 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.83 · 4 PDB
- Residue 147
- the 'disordered' region; a UniProt-annotated variant site (in stl6); the 'triple-helical region 3 (col3)' region
Similar variants
- COL9A3 p.Pro147His Uncertain significance ★ ⚠ same residue
- COL9A3 c.148-1G>A Pathogenic ★★ same type
- COL9A3 c.148-2A>G Pathogenic ★★ same type
- COL9A3 c.184-2A>G Likely pathogenic ★★ same type
- COL9A3 p.Arg471Ter Pathogenic ★★ same type
- COL9A3 p.Arg577Ter Pathogenic/Likely pathogenic ★★ same type
- COL9A3 p.Arg90Ter Pathogenic/Likely pathogenic ★★ same type
- COL9A3 c.1009-5G>A Uncertain significance ★★ 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/col9a3-p-pro147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown