COL1A2 p.Pro533=
c.1599T>A · rs2484715568 · VCV2566488
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 6.19e-05%)
Conditions
1
Cardiovascular phenotype
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 0.43 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 6.873 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.19e-05%
Overall
6.19e-05%
1/1,614,226 alleles · very rare
exomes 1/1,461,872 · genomes 0/152,354 · joint denominator
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
- COL1A2
- Protein
- p.Pro533=
- Coding
- c.1599T>A
- MANE Select
- NM_000089
- dbSNP
- rs2484715568
- Type
- single nucleotide variant
- Location
- chr7:94413731 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.02 · 5 PDB
- Residue 533
- the 'disordered' region
Similar variants
- COL1A2 c.2565+1G>A Pathogenic ★★ same condition
- COL1A2 p.Ala1119Thr Pathogenic/Likely pathogenic ★★ same condition
- COL1A2 p.Gly259Ser Pathogenic/Likely pathogenic ★★ same condition
- COL1A2 p.Gly907Ser Pathogenic/Likely pathogenic ★★ same condition
- COL1A2 c.1251+2T>G Uncertain significance ★★ same condition
- COL1A2 c.1404+4A>C Uncertain significance ★★ same condition
- COL1A2 c.792+4A>T Uncertain significance ★★ same condition
- COL1A2 p.Ala1035Thr 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/col1a2-p-pro533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown