Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 33.5%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.7 | GERP -2.1 |
| Overall | ||
| CADD | 0.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
33.5%
East Asian · 13,657/40,712 alleles
Filtering AF
33.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 32.9%
Overall
5.44%
84,062/1,545,136 alleles · common
exomes 74,338/1,392,846 · genomes 9,724/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 33.5% | 3 |
| South Asian | 14.9% | 7 |
| Admixed American | 14.2% | 7 |
| Middle Eastern | 10.5% | 10 |
| Remaining individualsnot grpmax-eligible | 7.01% | 14 |
| Amishnot grpmax-eligible | 5.04% | 20 |
| African / African-American | 4.95% | 20 |
| Ashkenazi Jewishnot grpmax-eligible | 4.76% | 21 |
| Finnishnot grpmax-eligible | 4.53% | 22 |
| European (non-Finnish) | 3.35% | 30 |
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.Pro43=
- Coding
- c.129C>T
- MANE Select
- NM_001853
- dbSNP
- rs2273079
- Type
- single nucleotide variant
- Location
- chr20:62817617 (GRCh38)
- Gene constraint
- LOEUF 1.026 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.83 · 4 PDB
- Residue 43
- the 'disordered' region; the 'triple-helical region 3 (col3)' region
Similar variants
- 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
- COL9A3 c.1161+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-pro43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown