COL5A2 p.Pro775=
c.2325C>T · VCV4687234
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000271%, nfe)
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 0.68 | GERP 0.012, phastCons 1 |
| Overall | ||
| CADD | 9.585 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000271%
European (non-Finnish) · 3/1,105,900 alleles
Filtering AF
7.2e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2e-05%
Overall
0.000197%
3/1,525,052 alleles · very rare
exomes 2/1,382,162 · genomes 1/142,890 · 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
- COL5A2
- Protein
- p.Pro775=
- Coding
- c.2325C>T
- MANE Select
- NM_000393
- Type
- single nucleotide variant
- Location
- chr2:189057332 (GRCh38)
- Gene constraint
- LOEUF 0.106 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.15
- Residue 775
- the 'disordered' region
Similar variants
- COL5A2 c.1159-1G>A Likely pathogenic ★★ same type
- COL5A2 c.2391+5G>A Likely pathogenic ★★ same type
- COL5A2 c.369+1G>T Likely pathogenic ★★ same type
- COL5A2 p.Gly252Cys Pathogenic/Likely pathogenic ★★ same type
- COL5A2 p.Pro659= Pathogenic ★★ same type
- COL5A2 c.1005+4T>C Uncertain significance ★★ same type
- COL5A2 c.1618-7G>A Uncertain significance ★★ same type
- COL5A2 c.1716+5G>A Uncertain significance ★★ 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/col5a2-p-pro775 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown