COL9A1 p.Pro552=
c.1656T>C · rs80251646 · VCV195813
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 5.62%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
connective tissue disorder
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 -4.5 |
| Overall | ||
| CADD | 0.123 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.62%
East Asian · 2,523/44,880 alleles
Filtering AF
5.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.36%
Overall
0.377%
6,082/1,614,140 alleles · common
exomes 5,193/1,461,822 · genomes 889/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 5.62% | 18 |
| Admixed American | 4.44% | 23 |
| Remaining individualsnot grpmax-eligible | 0.765% | 131 |
| South Asian | 0.261% | 383 |
| African / African-American | 0.16% | 625 |
| European (non-Finnish) | 0.00517% | 19,344 |
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
- COL9A1
- Protein
- p.Pro552=
- Coding
- c.1656T>C
- MANE Select
- NM_001851
- dbSNP
- rs80251646
- Type
- single nucleotide variant
- Location
- chr6:70254972 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.72 · 5 PDB
- Residue 552
- the 'disordered' region; the 'triple-helical region (col2)' region; a UniProt-annotated variant site (in stl4)
Similar variants
- COL9A1 p.Pro552Leu Uncertain significance ★ ⚠ same residue
- COL9A1 p.Arg507Ter Pathogenic ★★ same condition
- COL9A1 p.Ala778Val Uncertain significance ★★ ⚠ same condition
- COL9A1 p.Ser647Arg Uncertain significance ★★ ⚠ same condition
- COL9A1 p.Thr537= Uncertain significance ★★ same condition
- COL9A1 c.1089+9C>G Benign/Likely benign ★★ same condition
- COL9A1 p.Asp225Val Benign/Likely benign ★★ ⚠ same condition
- COL9A1 p.Glu450Gly Benign/Likely benign ★★ same condition
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/col9a1-p-pro552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown