COL27A1 p.Pro830=
c.2490G>A · rs374233169 · VCV1155973
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00551%, sas)
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 -7.3 | GERP -3.8 |
| Overall | ||
| CADD | 1.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00551%
South Asian · 5/90,768 alleles
Filtering AF
0.00211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00137%
Overall
0.000958%
14/1,461,100 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00551% | 18,154 |
| Admixed American | 0.00167% | 59,954 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| African / African-American | 0.00133% | 75,020 |
| European (non-Finnish) | 0.000509% | 196,616 |
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
- COL27A1
- Protein
- p.Pro830=
- Coding
- c.2490G>A
- MANE Select
- NM_032888
- dbSNP
- rs374233169
- Type
- single nucleotide variant
- Location
- chr9:114231102 (GRCh38)
- Gene constraint
- LOEUF 0.539 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.13
- Residue 830
- the 'triple-helical region' region; the collagen-like 4 domain
Similar variants
- COL27A1 p.Pro830Gln Uncertain significance ★ ⚠ same residue
- COL27A1 p.Pro830Leu Uncertain significance ★ ⚠ same residue
- COL27A1 c.62+1G>T Likely pathogenic ★★ same type
- COL27A1 p.Arg1354Ter Pathogenic ★★ same type
- COL27A1 p.Arg707Ter Pathogenic ★★ same type
- COL27A1 p.Arg774Ter Pathogenic/Likely pathogenic ★★ same type
- COL27A1 p.Gln406Ter Pathogenic/Likely pathogenic ★★ same type
- COL27A1 p.Gly1147Ter Pathogenic/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/col27a1-p-pro830 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown