COP1 p.Lys589=
c.1767A>G · rs111531372 · VCV715553
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.944%, afr)
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 -0.97 | GERP -4.1, phastCons 0.006 |
| Overall | ||
| CADD | 3.092 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.944%
African / African-American · 707/74,914 alleles
Filtering AF
0.886%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.863%
Overall
0.0508%
816/1,607,570 alleles · rare
exomes 416/1,455,246 · genomes 400/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.944% | 106 |
| Remaining individualsnot grpmax-eligible | 0.0931% | 1,074 |
| Middle Eastern | 0.0662% | 1,512 |
| Admixed American | 0.0467% | 2,144 |
| South Asian | 0.00659% | 15,165 |
| European (non-Finnish) | 0.00111% | 90,312 |
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
- COP1
- Protein
- p.Lys589=
- Coding
- c.1767A>G
- MANE Select
- NM_022457
- dbSNP
- rs111531372
- Type
- single nucleotide variant
- Location
- chr1:175989442 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 75.64 · 7 PDB
Similar variants
- COP1 c.1142-7C>T Likely benign ★★ same type
- COP1 p.Arg295Thr Benign ★★ same type
- COP1 p.Met299Val Benign ★★ same type
- COP1 p.Ala117Val Uncertain significance ★ ⚠ same type
- COP1 p.Ala12Ser Uncertain significance ★ ⚠ same type
- COP1 p.Ala354Val Uncertain significance ★ ⚠ same type
- COP1 p.Ala457Val Uncertain significance ★ ⚠ same type
- COP1 p.Ala7Val 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/cop1-p-lys589 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown