COPA p.Ala307=
c.921A>G · rs1424115979 · VCV2639500
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -1.1 | GERP -5.3, phastCons 0.001 |
| Overall | ||
| CADD | 5.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000248%
4/1,613,728 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,468 |
| European (non-Finnish) | 0.00017% | 589,943 |
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
- COPA
- Protein
- p.Ala307=
- Coding
- c.921A>G
- MANE Select
- NM_004371
- dbSNP
- rs1424115979
- Type
- single nucleotide variant
- Location
- chr1:160313089 (GRCh38)
- Gene constraint
- LOEUF 0.098 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.85 · 3 PDB
- Residue 307
- a β-strand
Similar variants
- COPA p.Arg233His Pathogenic/Likely pathogenic ★★ same type
- COPA p.Glu241Lys Pathogenic ★★ same type
- COPA p.Ala111Thr Uncertain significance ★★ ⚠ same type
- COPA p.Ala176Val Uncertain significance ★★ ⚠ same type
- COPA p.Ala407Val Uncertain significance ★★ ⚠ same type
- COPA p.Ala422Thr Uncertain significance ★★ ⚠ same type
- COPA p.Ala469Val Uncertain significance ★★ ⚠ same type
- COPA p.Ala510Thr 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/copa-p-ala307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown