COL2A1 p.Pro1483=
c.4449G>A · rs41272771 · VCV516233
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, afr)
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 1.3 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 8.804 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
African / African-American · 854/74,972 alleles
Filtering AF
1.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.05%
Overall
0.0612%
988/1,614,074 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.14% | 88 |
| Admixed American | 0.09% | 1,111 |
| Remaining individualsnot grpmax-eligible | 0.0688% | 1,454 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.00297% | 33,715 |
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
- COL2A1
- Protein
- p.Pro1483=
- Coding
- c.4449G>A
- MANE Select
- NM_001844
- dbSNP
- rs41272771
- Type
- single nucleotide variant
- Location
- chr12:47973422 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 11 PDB
- Residue 1483
- the fibrillar collagen nc1 domain; a disulfide bond
Similar variants
- COL2A1 p.Pro1483Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL2A1 p.Arg533Ter Pathogenic ★★ same condition
- COL2A1 p.Gly1197Ser Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 p.Gly621Glu Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 p.Gly669Ser Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 p.Gly984Arg Likely pathogenic ★★ same condition
- COL2A1 p.Arg719His Uncertain significance ★★ ⚠ same condition
- COL2A1 p.Arg940Pro Uncertain significance ★★ ⚠ 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/col2a1-p-pro1483 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown