COPB2 p.Val477=
c.1431C>G · rs750780564 · VCV1519034
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0486%, amr)
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 2.6 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 7.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0486%
Admixed American · 29/59,696 alleles
Filtering AF
0.0347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.03%
Overall
0.00267%
43/1,612,506 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0486% | 2,058 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,676 |
| African / African-American | 0.00401% | 24,953 |
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.Val477=
- Coding
- c.1431C>G
- MANE Select
- NM_004766
- dbSNP
- rs750780564
- Type
- single nucleotide variant
- Location
- chr3:139368259 (GRCh38)
- Gene constraint
- LOEUF 0.177 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.75 · 2 PDB
- Residue 477
- a β-strand
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-val477 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown