COL1A1 p.Pro313=
c.939T>A · rs1404720366 · VCV1766799
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
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 1.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 10.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,870 alleles
Overall
0.000124%
2/1,610,752 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,870 |
| European (non-Finnish) | 8.49e-05% | 1,178,306 |
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
- COL1A1
- Protein
- p.Pro313=
- Coding
- c.939T>A
- MANE Select
- NM_000088
- dbSNP
- rs1404720366
- Type
- single nucleotide variant
- Location
- chr17:50196332 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.26 · 14 PDB
- Residue 313
- the 'disordered' region; a modified residue (4-hydroxyproline); the 'triple-helical region' region
Similar variants
- COL1A1 p.Pro313Ser Uncertain significance ★★ ⚠ same residue
- COL1A1 p.Pro313Thr Uncertain significance ★ ⚠ same residue
- COL1A1 c.1299+5G>A Pathogenic/Likely pathogenic ★★ same condition
- COL1A1 p.Arg1141Ter Pathogenic ★★ same condition
- COL1A1 p.Gly188Asp Pathogenic/Likely pathogenic ★★ same condition
- COL1A1 p.Gly200Val Pathogenic/Likely pathogenic ★★ same condition
- COL1A1 p.Met181Ile Pathogenic/Likely pathogenic ★★ same condition
- COL1A1 p.Pro313fs Pathogenic ★★ same residue
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/col1a1-p-pro313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown