COPB2 p.Pro862=
c.2586G>A · rs141832843 · VCV1622752
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.711%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.015 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.76 | GERP -4.2, phastCons 0.013 |
| Overall | ||
| CADD | 8.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.711%
African / African-American · 533/74,986 alleles
Filtering AF
0.661%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.641%
Overall
0.0609%
983/1,614,028 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.711% | 141 |
| Admixed American | 0.257% | 390 |
| Middle Eastern | 0.165% | 606 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0676% | 1,480 |
| European (non-Finnish) | 0.0164% | 6,082 |
| East Asian | 0.0156% | 6,411 |
| South Asian | 0.00769% | 13,010 |
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
- COPB2
- Protein
- p.Pro862=
- Coding
- c.2586G>A
- MANE Select
- NM_004766
- dbSNP
- rs141832843
- Type
- single nucleotide variant
- Location
- chr3:139358239 (GRCh38)
- Gene constraint
- LOEUF 0.177 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.75 · 2 PDB
- Residue 862
- the 'disordered' region
Similar variants
- COPB2 p.Glu646Lys Uncertain significance ★★ ⚠ same type
- COPB2 p.Glu879Lys Uncertain significance ★★ ⚠ same type
- COPB2 p.Ile864Thr Uncertain significance ★★ ⚠ same type
- COPB2 p.Leu649Phe Uncertain significance ★★ ⚠ same type
- COPB2 p.Ser135Ala Uncertain significance ★★ ⚠ same type
- COPB2 c.1095-23T>C Benign ★★ same type
- COPB2 c.1401+12C>T Likely benign ★★ same type
- COPB2 c.141+20G>T 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/copb2-p-pro862 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown