COPG1 p.Pro287=
c.861G>A · rs77129536 · VCV789714
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.8%, afr) — too common for a highly-penetrant pathogenic allele
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 -20 | GERP -3.2 |
| Overall | ||
| CADD | 0.184 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.8%
African / African-American · 4,352/74,998 alleles
Filtering AF
5.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.6%
Overall
0.518%
8,360/1,613,242 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.8% | 17 |
| South Asian | 0.931% | 107 |
| Remaining individualsnot grpmax-eligible | 0.513% | 195 |
| Admixed American | 0.423% | 236 |
| Ashkenazi Jewishnot grpmax-eligible | 0.419% | 239 |
| Middle Eastern | 0.387% | 258 |
| European (non-Finnish) | 0.207% | 484 |
| East Asian | 0.00446% | 22,444 |
| Finnishnot grpmax-eligible | 0.00156% | 63,990 |
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
- COPG1
- Protein
- p.Pro287=
- Coding
- c.861G>A
- MANE Select
- NM_016128
- dbSNP
- rs77129536
- Type
- single nucleotide variant
- Location
- chr3:129257850 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.09 · 1 PDB
Similar variants
- COPG1 p.Arg247His Uncertain significance ★★ ⚠ same type
- COPG1 p.Leu864Met Uncertain significance ★★ ⚠ same type
- COPG1 p.Thr64Met Uncertain significance ★★ ⚠ same type
- COPG1 c.91-11T>C Benign ★★ same type
- COPG1 c.939+13C>G Benign ★★ same type
- COPG1 p.His221= Benign ★★ same type
- COPG1 p.Ile92= Benign/Likely benign ★★ same type
- COPG1 p.Leu240Val Benign/Likely benign ★★ ⚠ 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/copg1-p-pro287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown