COL9A1 p.Pro384=
c.1152T>A · rs1562316541 · VCV2158547
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.66 | GERP 0.72, phastCons 0.9 |
| Overall | ||
| CADD | 10.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- COL9A1
- Protein
- p.Pro384=
- Coding
- c.1152T>A
- MANE Select
- NM_001851
- dbSNP
- rs1562316541
- Type
- single nucleotide variant
- Location
- chr6:70270359 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.72 · 5 PDB
- Residue 384
- the 'disordered' region; the 'triple-helical region (col3)' region; a UniProt-annotated variant site (in stl4); the collagen-like 3 domain
Similar variants
- COL9A1 p.Pro384Ser Uncertain significance ★★ ⚠ same residue
- COL9A1 c.1665+2T>C Likely pathogenic ★★ same type
- COL9A1 p.Arg471Ter Pathogenic/Likely pathogenic ★★ same type
- COL9A1 p.Arg507Ter Pathogenic ★★ same type
- COL9A1 p.Gln750Ter Pathogenic/Likely pathogenic ★★ same type
- COL9A1 p.Glu374Ter Pathogenic/Likely pathogenic ★★ same type
- COL9A1 p.Lys139Ter Pathogenic/Likely pathogenic ★★ same type
- COL9A1 p.Ser351Ter 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/col9a1-p-pro384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown